5GO3 | pdb_00005go3

Crystal structure of a di-nucleotide cyclase Vibrio mutant

• PDB DOI: https://doi.org/10.2210/pdb5GO3/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-07-26 Released: 2016-11-02 
• Deposition Author(s): Ming, Z.H., Wang, W., Xie, Y.C., Chen, Y.C., Yan, L.M., Lou, Z.Y.
• Funding Organization(s): National Basic Research Program of China, National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.292 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Literature

Crystal structure of a di-nucleotide cyclase Vibrio mutant

Ming, Z.H., Wang, W., Xie, Y.C., Chen, Y.C., Yan, L.M., Lou, Z.Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 101.34 kDa 
• Atom Count: 6,104 
• Modeled Residue Count: 726 
• Deposited Residue Count: 894 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic GMP-AMP synthase	A, B	447	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 2  Gene Names: dncV, VC_0179 EC: 2.7.7
UniProt
Find proteins for Q9KVG7 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KVG7  Go to UniProtKB:  Q9KVG7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.292 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.745	α = 90
b = 46.272	β = 99.82
c = 121.791	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-11-02 
Deposition Author(s): Ming, Z.H., Wang, W., Xie, Y.C., Chen, Y.C., Yan, L.M., Lou, Z.Y.

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Funding Organization	Location	Grant Number
National Basic Research Program of China	China	2013CB911103
National Basic Research Program of China	China	2012CB518904
National Natural Science Foundation of China	China	81322023
National Natural Science Foundation of China	China	31170678
National Natural Science Foundation of China	China	31170158
National Natural Science Foundation of China	China	31370733
National Natural Science Foundation of China	China	31000332

Revision History  

• Version 1.0: 2016-11-02
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary