3I99 | pdb_00003i99

The crystal structure of the UDP-N-acetylenolpyruvoylglucosamine reductase from the Vibrio cholerae O1 biovar Tor

• PDB DOI: https://doi.org/10.2210/pdb3I99/pdb

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


• Deposited: 2009-07-10 Released: 2009-10-20 
• Deposition Author(s): Zhang, R., Gu, M., Peterson, S., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.223 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

The crystal structure of the UDP-N-acetylenolpyruvoylglucosamine reductase from the Vibrio cholerae O1 biovar Tor

Zhang, R., Gu, M., Peterson, S., Anderson, W., Joachimiak, A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 40.79 kDa 
• Atom Count: 2,803 
• Modeled Residue Count: 340 
• Deposited Residue Count: 357 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylenolpyruvoylglucosamine reductase	A	357	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: gi: 15640345, murB, VCM66_0302 EC: 1.1.1.158 (PDB Primary Data), 1.3.1.98 (UniProt)
UniProt
Find proteins for Q9KV40 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KV40  Go to UniProtKB:  Q9KV40

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
PO4	C [auth A], D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.223 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.334	α = 90
b = 84.334	β = 90
c = 53.335	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-20 
Deposition Author(s): Zhang, R., Gu, M., Peterson, S., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary