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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.292 (Depositor), 0.282 (DCC)
R-Value Work:
0.228 (Depositor), 0.228 (DCC)
R-Value Observed:
0.231 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KVG7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.292 (Depositor), 0.282 (DCC)
R-Value Work: 0.228 (Depositor), 0.228 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-11-02

Deposition Author(s):

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 (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.