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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Kumagai, T."

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Search Summary

This query matches 20 Structures.

Refinements

Structure Determination Methodology

experimental (20)

Scientific Name of Source Organism

	Streptomyces castaneoglobisporus (6)
	Klebsiella pneumoniae (3)
	Streptomyces lavendulae (3)
	Streptomyces verticillus (3)
	Streptomyces caespitosus (2)
	Streptomyces lavendulae subsp. lavendulae (2)
	Enterococcus mundtii (1)

Taxonomy

Bacteria (20)

Experimental Method

	X-RAY DIFFRACTION (19)
	SOLUTION NMR (1)

Polymer Entity Type

Protein (20)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (13)
	2.0 - 2.5 (3)
	2.5 - 3.0 (1)

Release Date

	2000 - 2004 (9)
	2005 - 2009 (9)
	2010 - 2014 (2)

Enzyme Classification Name

	Oxidoreductases (6)
	Transferases (2)
	Isomerases (3)

Symmetry Type

	Cyclic (13)
	Asymmetric (7)

SCOP Classification

	Alpha and beta proteins (a+b) (14)
	Artifacts (11)
	Alpha and beta proteins (a/b) (5)
	All alpha proteins (6)
	All beta proteins (3)

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1 to 20 of 20 Structures

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1ECS \| pdb_00001ecs	Download File View File

THE 1.7 A CRYSTAL STRUCTURE OF A BLEOMYCIN RESISTANCE DETERMINANT ENCODED ON THE TRANSPOSON TN5

Maruyama, M., Matoba, Y., Kumagai, T., Sugiyama, M.

(2001) J Biological Chem 276: 9992-9999

Released	2001-05-02
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Klebsiella pneumoniae
Macromolecule	BLEOMYCIN RESISTANCE PROTEIN (protein)
Unique Ligands	CA, PG4

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1EWJ \| pdb_00001ewj	Download File View File

CRYSTAL STRUCTURE OF BLEOMYCIN-BINDING PROTEIN COMPLEXED WITH BLEOMYCIN

Maruyama, M., Kumagai, T., Matoba, Y., Hata, Y., Sugiyama, M.

(2001) J Biological Chem 276: 9992-9999

Released	2001-04-26
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Klebsiella pneumoniae
Macromolecule	BLEOMYCIN RESISTANCE DETERMINANT (protein)
Unique Ligands	BLM

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1JIE \| pdb_00001jie	Download File View File

Crystal structure of bleomycin-binding protein from bleomycin-producing Streptomyces verticillus complexed with metal-free bleomycin

Sugiyama, M., Kumagai, T., Hayashida, M., Maruyama, M., Matoba, Y.

(2002) J Biological Chem 277: 2311-2320

Released	2002-02-06
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Streptomyces verticillus
Macromolecule	bleomycin-binding protein (protein)
Unique Ligands	BLM

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1JIF \| pdb_00001jif	Download File View File

Crystal structure of bleomycin-binding protein from bleomycin-producing Streptomyces verticillus complexed with copper(II)-bleomycin

Sugiyama, M., Kumagai, T., Hayashida, M., Maruyama, M., Matoba, Y.

(2002) J Biological Chem 277: 2311-2320

Released	2002-02-06
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Streptomyces verticillus
Macromolecule	bleomycin-binding protein (protein)
Unique Ligands	BLM, CL, CU

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1MH6 \| pdb_00001mh6	Download File View File

Solution Structure of the Transposon Tn5-encoding Bleomycin-binding Protein, BLMT

Kumagai, T., Ohtani, K., Tsuboi, Y., Koike, T., Sugiyama, M.

To be published

Released	2003-02-19
Method	SOLUTION NMR
Organisms	Klebsiella pneumoniae
Macromolecule	BLEOMYCIN RESISTANCE PROTEIN (protein)

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1QTO \| pdb_00001qto	Download File View File

1.5 A CRYSTAL STRUCTURE OF A BLEOMYCIN RESISTANCE DETERMINANT FROM BLEOMYCIN-PRODUCING STREPTOMYCES VERTICILLUS

Kawano, Y., Kumagai, T., Muta, K., Matoba, Y., Davies, J., Sugiyama, M.

(2000) J Mol Biology 295: 915-925

Released	2000-06-28
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Streptomyces verticillus
Macromolecule	BLEOMYCIN-BINDING PROTEIN (protein)

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1VFH \| pdb_00001vfh	Download File View File

Crystal structure of alanine racemase from D-cycloserine producing Streptomyces lavendulae

Noda, M., Matoba, Y., Kumagai, T., Sugiyama, M.

(2004) J Biological Chem 279: 46153-46161

Released	2004-09-14
Method	X-RAY DIFFRACTION 2 Å
Organisms	Streptomyces lavendulae
Macromolecule	alanine racemase (protein)
Unique Ligands	PLP

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1VFS \| pdb_00001vfs	Download File View File

Crystal structure of D-cycloserine-bound form of alanine racemase from D-cycloserine-producing Streptomyces lavendulae

Noda, M., Matoba, Y., Kumagai, T., Sugiyama, M.

(2004) J Biological Chem 279: 46153-46161

Released	2004-09-14
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Streptomyces lavendulae
Macromolecule	alanine racemase (protein)
Unique Ligands	CL, DCS

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1VFT \| pdb_00001vft	Download File View File

Crystal structure of L-cycloserine-bound form of alanine racemase from D-cycloserine-producing Streptomyces lavendulae

Noda, M., Matoba, Y., Kumagai, T., Sugiyama, M.

(2004) J Biological Chem 279: 46153-46161

Released	2004-09-14
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Streptomyces lavendulae
Macromolecule	alanine racemase (protein)
Unique Ligands	CL, DCS

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1WX2 \| pdb_00001wx2	Download File View File

Crystal Structure of the oxy-form of the copper-bound Streptomyces castaneoglobisporus tyrosinase complexed with a caddie protein prepared by the addition of hydrogenperoxide

Matoba, Y., Kumagai, T., Yamamoto, A., Yoshitsu, H., Sugiyama, M.

(2006) J Biological Chem 281: 8981-8990

Released	2006-01-31
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Streptomyces castaneoglobisporus
Macromolecule	MelC (protein) tyrosinase (protein)
Unique Ligands	CU, NO3, PER

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1WX4 \| pdb_00001wx4	Download File View File

Crystal structure of the oxy-form of the copper-bound Streptomyces castaneoglobisporus tyrosinase complexed with a caddie protein prepared by the addition of dithiothreitol

Matoba, Y., Kumagai, T., Yamamoto, A., Yoshitsu, H., Sugiyama, M.

(2006) J Biological Chem 281: 8981-8990

Released	2006-01-31
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Streptomyces castaneoglobisporus
Macromolecule	MelC (protein) tyrosinase (protein)
Unique Ligands	CU, NO3, PER

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1WX5 \| pdb_00001wx5	Download File View File

Crystal Structure of the copper-free Streptomyces castaneoglobisporus tyrosinase complexed with a caddie protein in the monoclinic crystal

Matoba, Y., Kumagai, T., Yamamoto, A., Yoshitsu, H., Sugiyama, M.

(2006) J Biological Chem 281: 8981-8990

Released	2006-01-31
Method	X-RAY DIFFRACTION 2.02 Å
Organisms	Streptomyces castaneoglobisporus
Macromolecule	MelC (protein) tyrosinase (protein)
Unique Ligands	CL, NA

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1WXC \| pdb_00001wxc	Download File View File

Crystal Structure of the copper-free Streptomyces castaneoglobisporus tyrosinase complexed with a caddie protein

Matoba, Y., Kumagai, T., Yamamoto, A., Yoshitsu, H., Sugiyama, M.

(2006) J Biological Chem 281: 8981-8990

Released	2006-01-31
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	Streptomyces castaneoglobisporus
Macromolecule	MelC (protein) tyrosinase (protein)
Unique Ligands	NO3

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2A4W \| pdb_00002a4w	Download File View File

Crystal Structure Of Mitomycin C-Binding Protein Complexed with Copper(II)-Bleomycin A2

Danshiitsoodol, N., de Pinho, C.A., Matoba, Y., Kumagai, T., Sugiyama, M.

(2006) J Mol Biology 360: 398-408

Released	2006-07-18
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Streptomyces caespitosus
Macromolecule	Mitomycin-Binding Protein (protein)
Unique Ligands	BLM, CU

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2A4X \| pdb_00002a4x	Download File View File

Crystal Structure Of Mitomycin C-Binding Protein Complexed with Metal-Free Bleomycin A2

Danshiitsoodol, N., de Pinho, C.A., Matoba, Y., Kumagai, T., Sugiyama, M.

(2006) J Mol Biology 360: 398-408

Released	2006-07-18
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Streptomyces caespitosus
Macromolecule	Mitomycin-Binding Protein (protein)
Unique Ligands	BLM

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2AHK \| pdb_00002ahk	Download File View File

Crystal structure of the met-form of the copper-bound Streptomyces castaneoglobisporus tyrosinase in complex with a caddie protein obtained by soking in cupric sulfate for 6 months

Matoba, Y., Kumagai, T., Yamamoto, A., Yoshitsu, H., Sugiyama, M.

(2006) J Biological Chem 281: 8981-8990

Released	2006-01-31
Method	X-RAY DIFFRACTION 1.71 Å
Organisms	Streptomyces castaneoglobisporus
Macromolecule	CADDIE PROTEIN ORF378 (protein) TYROSINASE (protein)
Unique Ligands	CU, NO3

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2AHL \| pdb_00002ahl	Download File View File

Crystal structure of the hydroxylamine-induced deoxy-form of the copper-bound Streptomyces castaneoglobisporus tyrosinase in complex with a caddie protein

Matoba, Y., Kumagai, T., Yamamoto, A., Yoshitsu, H., Sugiyama, M.

(2006) J Biological Chem 281: 8981-8990

Released	2006-01-31
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Streptomyces castaneoglobisporus
Macromolecule	CADDIE PROTEIN ORF378 (protein) TYROSINASE (protein)
Unique Ligands	CU1, NO3

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2ZRR \| pdb_00002zrr	Download File View File

Crystal structure of an immunity protein that contributes to the self-protection of bacteriocin-producing Enterococcus mundtii 15-1A

Jeon, H.J., Noda, M., Matoba, Y., Kumagai, T., Sugiyama, M.

(2009) Biochem Biophys Res Commun 378: 574-578

Released	2009-02-17
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Enterococcus mundtii
Macromolecule	Mundticin KS immunity protein (protein)

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3VVL \| pdb_00003vvl	Download File View File

Crystal structure of L-serine-O-acetyltransferase found in D-cycloserine biosynthetic pathway

Oda, K., Matoba, Y., Kumagai, T., Noda, M., Sugiyama, M.

(2013) J Bacteriol 195: 1741-1749

Released	2013-03-20
Method	X-RAY DIFFRACTION 1.81 Å
Organisms	Streptomyces lavendulae subsp. lavendulae
Macromolecule	Homoserine O-acetyltransferase (protein)

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3VVM \| pdb_00003vvm	Download File View File

Crystal structure of G52A-P55G mutant of L-serine-O-acetyltransferase found in D-cycloserine biosynthetic pathway

Oda, K., Matoba, Y., Kumagai, T., Noda, M., Sugiyama, M.

(2013) J Bacteriol 195: 1741-1749

Released	2013-03-20
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Streptomyces lavendulae subsp. lavendulae
Macromolecule	Homoserine O-acetyltransferase (protein)

1 to 20 of 20 Structures

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1ECS | pdb_00001ecs

THE 1.7 A CRYSTAL STRUCTURE OF A BLEOMYCIN RESISTANCE DETERMINANT ENCODED ON THE TRANSPOSON TN5

1EWJ | pdb_00001ewj

CRYSTAL STRUCTURE OF BLEOMYCIN-BINDING PROTEIN COMPLEXED WITH BLEOMYCIN

1JIE | pdb_00001jie

Crystal structure of bleomycin-binding protein from bleomycin-producing Streptomyces verticillus complexed with metal-free bleomycin

1JIF | pdb_00001jif

Crystal structure of bleomycin-binding protein from bleomycin-producing Streptomyces verticillus complexed with copper(II)-bleomycin

1MH6 | pdb_00001mh6

Solution Structure of the Transposon Tn5-encoding Bleomycin-binding Protein, BLMT

1QTO | pdb_00001qto

1.5 A CRYSTAL STRUCTURE OF A BLEOMYCIN RESISTANCE DETERMINANT FROM BLEOMYCIN-PRODUCING STREPTOMYCES VERTICILLUS

1VFH | pdb_00001vfh

Crystal structure of alanine racemase from D-cycloserine producing Streptomyces lavendulae

1VFS | pdb_00001vfs

Crystal structure of D-cycloserine-bound form of alanine racemase from D-cycloserine-producing Streptomyces lavendulae

1VFT | pdb_00001vft

Crystal structure of L-cycloserine-bound form of alanine racemase from D-cycloserine-producing Streptomyces lavendulae

1WX2 | pdb_00001wx2

Crystal Structure of the oxy-form of the copper-bound Streptomyces castaneoglobisporus tyrosinase complexed with a caddie protein prepared by the addition of hydrogenperoxide

1WX4 | pdb_00001wx4

Crystal structure of the oxy-form of the copper-bound Streptomyces castaneoglobisporus tyrosinase complexed with a caddie protein prepared by the addition of dithiothreitol

1WX5 | pdb_00001wx5

Crystal Structure of the copper-free Streptomyces castaneoglobisporus tyrosinase complexed with a caddie protein in the monoclinic crystal

1WXC | pdb_00001wxc

Crystal Structure of the copper-free Streptomyces castaneoglobisporus tyrosinase complexed with a caddie protein

2A4W | pdb_00002a4w

Crystal Structure Of Mitomycin C-Binding Protein Complexed with Copper(II)-Bleomycin A2

2A4X | pdb_00002a4x

Crystal Structure Of Mitomycin C-Binding Protein Complexed with Metal-Free Bleomycin A2

2AHK | pdb_00002ahk

Crystal structure of the met-form of the copper-bound Streptomyces castaneoglobisporus tyrosinase in complex with a caddie protein obtained by soking in cupric sulfate for 6 months

2AHL | pdb_00002ahl

Crystal structure of the hydroxylamine-induced deoxy-form of the copper-bound Streptomyces castaneoglobisporus tyrosinase in complex with a caddie protein

2ZRR | pdb_00002zrr

Crystal structure of an immunity protein that contributes to the self-protection of bacteriocin-producing Enterococcus mundtii 15-1A

3VVL | pdb_00003vvl

Crystal structure of L-serine-O-acetyltransferase found in D-cycloserine biosynthetic pathway

3VVM | pdb_00003vvm

Crystal structure of G52A-P55G mutant of L-serine-O-acetyltransferase found in D-cycloserine biosynthetic pathway

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

1ECS | pdb_00001ecs

1EWJ | pdb_00001ewj

1JIE | pdb_00001jie

1JIF | pdb_00001jif

1MH6 | pdb_00001mh6

1QTO | pdb_00001qto

1VFH | pdb_00001vfh

1VFS | pdb_00001vfs

1VFT | pdb_00001vft

1WX2 | pdb_00001wx2

1WX4 | pdb_00001wx4

1WX5 | pdb_00001wx5

1WXC | pdb_00001wxc

2A4W | pdb_00002a4w

2A4X | pdb_00002a4x

2AHK | pdb_00002ahk

2AHL | pdb_00002ahl

2ZRR | pdb_00002zrr

3VVL | pdb_00003vvl

3VVM | pdb_00003vvm