2OCD | pdb_00002ocd

Crystal structure of L-asparaginase I from Vibrio cholerae O1 biovar eltor str. N16961

• PDB DOI: https://doi.org/10.2210/pdb2OCD/pdb
• Entry: 2OCD supersedes: 2H7K

• Classification: HYDROLASE
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-12-20 Released: 2007-01-30 
• Deposition Author(s): Nocek, B., Wu, R., Osipiuk, J., Moy, S., Kim, Y., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.246 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Crystal structure of L-asparaginase I from Vibrio cholerae O1 biovar eltor str. N16961

Nocek, B., Wu, R., Moy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 150.29 kDa 
• Atom Count: 10,702 
• Modeled Residue Count: 1,321 
• Deposited Residue Count: 1,348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-asparaginase I	A, B, C, D	337	Vibrio cholerae	Mutation(s): 16  Gene Names: O1 biovar eltor EC: 3.5.1.1
UniProt
Find proteins for Q9KQK3 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KQK3  Go to UniProtKB:  Q9KQK3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	I [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	E [auth A], F [auth B], G [auth B], H [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.246 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.235	α = 90
b = 117.838	β = 91.44
c = 121.431	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-30 
Deposition Author(s): Nocek, B., Wu, R., Osipiuk, J., Moy, S., Kim, Y., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• This entry supersedes: 2H7K

Revision History  

• Version 1.0: 2007-01-30
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-11-06
  Changes: Structure summary