3DZC | pdb_00003dzc

2.35 Angstrom resolution structure of WecB (VC0917), a UDP-N-acetylglucosamine 2-epimerase from Vibrio cholerae.

• PDB DOI: https://doi.org/10.2210/pdb3DZC/pdb

• Classification: ISOMERASE
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-29 Released: 2008-08-12 
• Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Winsor, J., Papazisi, L., Kwon, K., Hasseman, J., Peterson, S.N., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.234 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

2.35 Angstrom resolution structure of WecB (VC0917), a UDP-N-acetylglucosamine 2-epimerase from Vibrio cholerae.

Minasov, G., Shuvalova, L., Dubrovska, I., Winsor, J., Papazisi, L., Kwon, K., Hasseman, J., Peterson, S.N., Anderson, W.F.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 87.8 kDa 
• Atom Count: 6,616 
• Modeled Residue Count: 746 
• Deposited Residue Count: 792 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine 2-epimerase	A, B	396	Vibrio cholerae	Mutation(s): 0  Gene Names: VC_0917 EC: 5.1.3.14
UniProt
Find proteins for Q9KTI5 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KTI5  Go to UniProtKB:  Q9KTI5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.234 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33dzc

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.391	α = 90
b = 88.127	β = 90
c = 132.193	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-12 
Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Winsor, J., Papazisi, L., Kwon, K., Hasseman, J., Peterson, S.N., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2008-08-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-12-14
  Changes: Structure summary
• Version 1.3: 2017-10-25
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description