1RZ3 | pdb_00001rz3

Structure of a Possible Uridine Kinase from Bacillus stearothermophilus

PDB DOI: https://doi.org/10.2210/pdb1RZ3/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Geobacillus stearothermophilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2003-12-23 Released: 2004-05-04
Deposition Author(s): Cuff, M.E., Joachimiak, A., Wu, R.-Y., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.238 (Depositor), 0.233 (DCC)
R-Value Work:
0.203 (Depositor), 0.199 (DCC)
R-Value Observed:
0.203 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure of hypothetical protein RBSTP0775 from Bacillus stearothermophilus

Cuff, M.E., Joachimiak, A., Wu, R.-Y.

To be published.

Macromolecule Content

Total Structure Weight: 24.59 kDa
Atom Count: 1,785
Modelled Residue Count: 184
Deposited Residue Count: 201
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein RBSTP0775	A	201	Geobacillus stearothermophilus	Mutation(s): 0 Gene Names: RBSTP0775
UniProt
Find proteins for P84134 (Geobacillus stearothermophilus) Explore P84134 Go to UniProtKB: P84134
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P84134
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.238 (Depositor), 0.233 (DCC)
R-Value Work: 0.203 (Depositor), 0.199 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.01	α = 90
b = 45.185	β = 90
c = 107.023	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
d*TREK	data reduction
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2004-05-04

Deposition Author(s):

Cuff, M.E.

Joachimiak, A.

Wu, R.-Y.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2004-05-04
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary

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Deposit Data

Help and Resources

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Structure of a Possible Uridine Kinase from Bacillus stearothermophilus

Structure of hypothetical protein RBSTP0775 from Bacillus stearothermophilus

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

1RZ3 | pdb_00001rz3