4R7T | pdb_00004r7t

Crystal structure of glucosamine-6-phosphate deaminase from Vibrio cholerae

• PDB DOI: https://doi.org/10.2210/pdb4R7T/pdb

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


• Deposited: 2014-08-28 Released: 2014-10-01 
• Deposition Author(s): Maltseva, N., Kim, Y., Kwon, K., Anderson, W.F., Joachimiak, A., CSGID, Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of glucosamine-6-phosphate deaminase from Vibrio cholerae

Maltseva, N., Kim, Y., Kwon, K., Anderson, W.F., Joachimiak, A., CSGID

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 92.03 kDa 
• Atom Count: 6,568 
• Modeled Residue Count: 795 
• Deposited Residue Count: 822 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosamine-6-phosphate deaminase	A, B, C	274	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: nagB, VC_A1025 EC: 3.5.99.6
UniProt
Find proteins for Q9KKS5 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KKS5  Go to UniProtKB:  Q9KKS5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	H [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth A], G [auth B], I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34r7t

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.359	α = 90
b = 135.124	β = 106.15
c = 86.001	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-01 
Deposition Author(s): Maltseva, N., Kim, Y., Kwon, K., Anderson, W.F., Joachimiak, A., CSGID, Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2014-10-01
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description