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233,249 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Perego, M."

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Search Summary

This query matches 14 Structures.

Refinements

Structure Determination Methodology

experimental (14)

Scientific Name of Source Organism

	Homo sapiens (5)
	Streptomyces ficellus (3)
	Escherichia coli (2)
	Pyrococcus horikoshii OT3 (2)
	Streptomyces sahachiroi (2)

Taxonomy

	Bacteria (7)
	Eukaryota (5)
	Archaea (2)

Experimental Method

	SOLUTION NMR (7)
	X-RAY DIFFRACTION (7)

Polymer Entity Type

	Protein (14)
	DNA (2)

Refinement Resolution (Å)

	1.5 - 2.0 (6)
	2.5 - 3.0 (1)

Release Date

	2000 - 2004 (6)
	2005 - 2009 (3)
	2020 - 2024 (5)

Symmetry Type

	Asymmetric (7)
	Cyclic (5)
	Dihedral (2)

SCOP Classification

	All alpha proteins (6)
	Small proteins (1)

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1 to 14 of 14 Structures

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1D8J \| pdb_00001d8j	Download File View File

SOLUTION STRUCTURE OF THE CENTRAL CORE DOMAIN OF TFIIE BETA

Okuda, M., Watanabe, Y., Okamura, H., Hanaoka, F., Ohkuma, Y., Nishimura, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2000) EMBO J 19: 1346-1356

Released	2000-04-26
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	GENERAL TRANSCRIPTION FACTOR TFIIE-BETA (protein)

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1D8K \| pdb_00001d8k	Download File View File

SOLUTION STRUCTURE OF THE CENTRAL CORE DOMAIN OF TFIIE BETA

Okuda, M., Watanabe, Y., Okamura, H., Hanaoka, F., Ohkuma, Y., Nishimura, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2000) EMBO J 19: 1346-1356

Released	2000-04-26
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	GENERAL TRANSCRIPTION FACTOR TFIIE-BETA (protein)

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1ITY \| pdb_00001ity	Download File View File

Solution structure of the DNA binding domain of human TRF1

Nishikawa, T., Okamura, H., Nagadoi, A., Konig, P., Rhodes, D., Nishimura, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2001) Structure 9: 1237-1251

Released	2002-03-06
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	TRF1 (protein)

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1IV6 \| pdb_00001iv6	Download File View File

Solution Structure of the DNA Complex of Human TRF1

Nishikawa, T., Okamura, H., Nagadoi, A., Konig, P., Rhodes, D., Nishimura, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2001) Structure 9: 1237-1251

Released	2002-04-17
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	TELOMERIC REPEAT BINDING FACTOR 1 (protein) 5'-D(CPCPCPTPAPAPCPCPCPTPAPAPC)-3' (nucleic acid) 5'-D(GPTPTPAPGPGPGPTPTPAPGPGPG)-3' (nucleic acid)

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1QQI \| pdb_00001qqi	Download File View File

SOLUTION STRUCTURE OF THE DNA-BINDING AND TRANSACTIVATION DOMAIN OF PHOB FROM ESCHERICHIA COLI

Okamura, H., Hanaoka, S., Nagadoi, A., Makino, K., Nishimura, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2000) J Mol Biology 295: 1225-1236

Released	2000-06-07
Method	SOLUTION NMR
Organisms	Escherichia coli
Macromolecule	PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB (protein)

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1VD4 \| pdb_00001vd4	Download File View File

Solution structure of the zinc finger domain of TFIIE alpha

Okuda, M., Tanaka, A., Arai, Y., Satoh, M., Okamura, H., Nagadoi, A., Hanaoka, F., Ohkuma, Y., Nishimura, Y.

(2004) J Biological Chem 279: 51395-51403

Released	2004-10-05
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Transcription initiation factor IIE, alpha subunit (protein)
Unique Ligands	ZN

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2E1A \| pdb_00002e1a	Download File View File

crystal structure of FFRP-DM1

Koike, H., Suzuki, M.

(2007) Structure 15: 1325-1338

Released	2007-09-18
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	75aa long hypothetical regulatory protein AsnC (protein)
Unique Ligands	MSE

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2Z33 \| pdb_00002z33	Download File View File

Solution structure of the DNA complex of PhoB DNA-binding/transactivation Domain

Yamane, T., Okamura, H., Ikeguchi, M., Nishimura, Y., Kidera, A.

(2008) Proteins 71: 1970-1983

Released	2008-04-22
Method	SOLUTION NMR
Organisms	Escherichia coli
Macromolecule	Phosphate regulon transcriptional regulatory protein phoB (protein) 5'-D(APCPAPGPAPTPTPTPAPTPGPAPCPAPGPT)-3' (nucleic acid) 5'-D(APCPTPGPTPCPAPTPAPAPAPTPCPTPGPT)-3' (nucleic acid)

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2Z4P \| pdb_00002z4p	Download File View File

Crystal structure of FFRP-DM1

Yamada, M., Koike, H., Kudo, N., Suzuki, M.

(2007) Structure 15: 1325-1338

Released	2007-09-18
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	75aa long hypothetical regulatory protein AsnC (protein)
Unique Ligands	ILE

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7WUW \| pdb_00007wuw	Download File View File

Crystal structure of AziU3/U2 from Streptomyces sahachiroi

Kurosawa, S., Yoshida, A., Tomita, T., Nishiyama, M.

(2022) J Am Chem Soc 144: 16164-16170

Released	2022-09-07
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Streptomyces sahachiroi
Macromolecule	AziU2 (protein) AziU3 (protein)
Unique Ligands	MG, PG4

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7WUX \| pdb_00007wux	Download File View File

Crystal structure of AziU3/U2 complexed with (5S,6S)-O7-sulfo DADH from Streptomyces sahachiroi

Kurosawa, S., Yoshida, A., Tomita, T., Nishiyama, M.

(2022) J Am Chem Soc 144: 16164-16170

Released	2022-09-07
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Streptomyces sahachiroi
Macromolecule	AziU2 (protein) AziU3 (protein)
Unique Ligands	6OI, MG, P4G, PGE

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8GYH \| pdb_00008gyh	Download File View File

Crystal structure of Fic25 (apo form) from Streptomyces ficellus

Kurosawa, S., Yoshida, A., Tomita, T., Nishiyama, M.

(2023) ACS Chem Biol 18: 385-395

Released	2023-02-22
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Streptomyces ficellus
Macromolecule	DegT/DnrJ/EryC1/StrS family aminotransferase (protein)
Unique Ligands	GOL, IMD

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8GYI \| pdb_00008gyi	Download File View File

Crystal structure of Fic25 (holo form) from Streptomyces ficellus

Kurosawa, S., Yoshida, A., Tomita, T., Nishiyama, M.

(2023) ACS Chem Biol 18: 385-395

Released	2023-02-22
Method	X-RAY DIFFRACTION 1.93 Å
Organisms	Streptomyces ficellus
Macromolecule	DegT/DnrJ/EryC1/StrS family aminotransferase (protein)
Unique Ligands	GOL, IMD, PLP

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8GYJ \| pdb_00008gyj	Download File View File

Crystal structure of Fic25 complexed with PLP-(5S,6S)-N2-acetyl-DADH adduct from Streptomyces ficellus

Kurosawa, S., Yoshida, A., Tomita, T., Nishiyama, M.

(2023) ACS Chem Biol 18: 385-395

Released	2023-02-22
Method	X-RAY DIFFRACTION 1.82 Å
Organisms	Streptomyces ficellus
Macromolecule	DegT/DnrJ/EryC1/StrS family aminotransferase (protein)
Unique Ligands	GOL, IMD, KKX

1 to 14 of 14 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

1D8J | pdb_00001d8j

SOLUTION STRUCTURE OF THE CENTRAL CORE DOMAIN OF TFIIE BETA

1D8K | pdb_00001d8k

SOLUTION STRUCTURE OF THE CENTRAL CORE DOMAIN OF TFIIE BETA

1ITY | pdb_00001ity

Solution structure of the DNA binding domain of human TRF1

1IV6 | pdb_00001iv6

Solution Structure of the DNA Complex of Human TRF1

1QQI | pdb_00001qqi

SOLUTION STRUCTURE OF THE DNA-BINDING AND TRANSACTIVATION DOMAIN OF PHOB FROM ESCHERICHIA COLI

1VD4 | pdb_00001vd4

Solution structure of the zinc finger domain of TFIIE alpha

2E1A | pdb_00002e1a

crystal structure of FFRP-DM1

2Z33 | pdb_00002z33

Solution structure of the DNA complex of PhoB DNA-binding/transactivation Domain

2Z4P | pdb_00002z4p

Crystal structure of FFRP-DM1

7WUW | pdb_00007wuw

Crystal structure of AziU3/U2 from Streptomyces sahachiroi

7WUX | pdb_00007wux

Crystal structure of AziU3/U2 complexed with (5S,6S)-O7-sulfo DADH from Streptomyces sahachiroi

8GYH | pdb_00008gyh

Crystal structure of Fic25 (apo form) from Streptomyces ficellus

8GYI | pdb_00008gyi

Crystal structure of Fic25 (holo form) from Streptomyces ficellus

8GYJ | pdb_00008gyj

Crystal structure of Fic25 complexed with PLP-(5S,6S)-N2-acetyl-DADH adduct from Streptomyces ficellus

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Symmetry Type

SCOP Classification

1D8J | pdb_00001d8j

1D8K | pdb_00001d8k

1ITY | pdb_00001ity

1IV6 | pdb_00001iv6

1QQI | pdb_00001qqi

1VD4 | pdb_00001vd4

2E1A | pdb_00002e1a

2Z33 | pdb_00002z33

2Z4P | pdb_00002z4p

7WUW | pdb_00007wuw

7WUX | pdb_00007wux

8GYH | pdb_00008gyh

8GYI | pdb_00008gyi

8GYJ | pdb_00008gyj