2GU1

Crystal structure of a zinc containing peptidase from vibrio cholerae

• PDB DOI: https://doi.org/10.2210/pdb2GU1/pdb

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


• Deposited: 2006-04-28 Released: 2006-07-04 
• Deposition Author(s): Sugadev, R., Kumaran, D., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.264 
• R-Value Work: 0.230 
• R-Value Observed: 0.230 

Literature

Crystal structure of a putative lysostaphin peptidase from Vibrio cholerae.

Ragumani, S., Kumaran, D., Burley, S.K., Swaminathan, S.

(2008) Proteins 72: 1096-1103

• PubMed: 18498110 
• DOI: https://doi.org/10.1002/prot.22095
• Primary Citation of Related Structures:  
  2GU1

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Organizational Affiliation: 

Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.77 kDa 
• Atom Count: 2,688 
• Modelled Residue Count: 324 
• Deposited Residue Count: 361 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc peptidase	A	361	Vibrio cholerae	Mutation(s): 0  EC: 3.4
UniProt
Find proteins for Q9KUL5 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KUL5  Go to UniProtKB:  Q9KUL5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.264 
• R-Value Work: 0.230 
• R-Value Observed: 0.230 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.382	α = 90
b = 85.396	β = 112.96
c = 53.404	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
SHARP	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-04 
Deposition Author(s): Sugadev, R., Kumaran, D., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2006-07-04
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references