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)

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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) 

Literature

Structure of hypothetical protein RBSTP0775 from Bacillus stearothermophilus

Cuff, M.E., Joachimiak, A., Wu, R.-Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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

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  

• 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