5HJ5

Crystal structure of tertiary complex of glucosamine-6-phosphate deaminase from Vibrio cholerae with BETA-D-GLUCOSE-6-PHOSPHATE and FRUCTOSE-6-PHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.137 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of tertiary complex of glucosamine-6-phosphate deaminase from Vibrio cholerae with BETA-D-GLUCOSE-6-PHOSPHATE and FRUCTOSE -6-PHOSPHATE

Chang, C.Maltseva, N.Kim, Y.Kwon, K.Anderson, W.F.Joachimiak, A.Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucosamine-6-phosphate deaminase
A, B, C, D
267Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 0 
Gene Names: nagBVC_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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KKS5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F6R
Query on F6R

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
N [auth C],
Q [auth D]
FRUCTOSE -6-PHOSPHATE
C6 H13 O9 P
GSXOAOHZAIYLCY-HSUXUTPPSA-N
BG6
Query on BG6

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
O [auth C],
R [auth D]
6-O-phosphono-beta-D-glucopyranose
C6 H13 O9 P
NBSCHQHZLSJFNQ-VFUOTHLCSA-N
GOL
Query on GOL

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G [auth A]
H [auth A]
I [auth A]
M [auth B]
P [auth C]
G [auth A],
H [auth A],
I [auth A],
M [auth B],
P [auth C],
S [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY
Query on ACY

Download Ideal Coordinates CCD File 
L [auth B]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.137 
  • Space Group: P 63
  • Diffraction Data: https://doi.org/10.18430/m35hj5
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.093α = 90
b = 113.093β = 90
c = 215.683γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
MOLREPphasing
Cootmodel building
SBC-Collectdata collection

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Refinement description, Structure summary