7LWZ | pdb_00007lwz

Apo Structure of Vibrio cholerae dGTPase protein VC1979

• PDB DOI: https://doi.org/10.2210/pdb7LWZ/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-03-02 Released: 2021-03-10 
• Deposition Author(s): Sikkema, A.P., Horng, J., Klemm, B.P., Schaaper, R.M., Hall, T.M.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 
  0.252 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Structure of Vibrio cholerae dGTPase protein VC1979

Sikkema, A.P., Horng, J., Klemm, B.P., Schaaper, R.M., Hall, T.M.T.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 301.31 kDa 
• Atom Count: 18,393 
• Modeled Residue Count: 2,340 
• Deposited Residue Count: 2,658 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyguanosinetriphosphate triphosphohydrolase-like protein 1	A [auth B], B [auth A], C [auth D], D [auth C], E [auth F], F [auth E]	443	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: VC_1979
UniProt
Find proteins for Q9KQL9 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KQL9  Go to UniProtKB:  Q9KQL9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	G [auth B], H [auth A], I [auth D], J [auth C], K [auth F], L [auth E]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free:  0.252 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.003	α = 90
b = 161.869	β = 90
c = 184.773	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-03-10 
Deposition Author(s): Sikkema, A.P., Horng, J., Klemm, B.P., Schaaper, R.M., Hall, T.M.T.

Revision History  

• Version 1.0: 2021-03-10
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description