3H2Y | pdb_00003h2y

Crystal structure of YqeH GTPase from Bacillus anthracis with dGDP bound

• PDB DOI: https://doi.org/10.2210/pdb3H2Y/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus anthracis str. Sterne
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-04-15 Released: 2009-06-16 
• Deposition Author(s): Brunzelle, J.S., Anderson, S.M., Xu, X., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.242 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Structure of YqeH GTPase from Bacillus anthracis with dGDP Bound

Brunzelle, J.S., Anderson, S.M., Wawrzak, Z., Xu, U., Cui, H., Savchenko, A., Anderson, W.F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 42.07 kDa 
• Atom Count: 2,587 
• Modeled Residue Count: 309 
• Deposited Residue Count: 368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase family protein	A	368	Bacillus anthracis str. Sterne	Mutation(s): 0  Gene Names: BAS4233, BA_4562, GBAA4562, GBAA_4562, YqeH
UniProt
Find proteins for A0A1J9WBB5 (Bacillus anthracis) Explore A0A1J9WBB5  Go to UniProtKB:  A0A1J9WBB5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGI	B [auth A]	2'-DEOXYGUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 CIKGWCTVFSRMJU-KVQBGUIXSA-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: 1.80 Å
• R-Value Free:  0.242 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33h2y

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.13	α = 90
b = 58.99	β = 99.38
c = 77.72	γ = 90

Software Package:

Software Name	Purpose
BLU-MAX	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-16 
Deposition Author(s): Brunzelle, J.S., Anderson, S.M., Xu, X., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-06-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-22
  Changes: Data collection
• Version 1.4: 2024-10-30
  Changes: Structure summary