5JZO | pdb_00005jzo

Structure of wild type amidase at high temperature at 2.5 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb5JZO/pdb

• Classification: LYASE
• Organism(s): Vibrio cholerae O395
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-05-17 Released: 2016-06-15 
• Deposition Author(s): Chowdhury, S.R., Sen, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.256 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Structure of wild type amidase at high temperature at 2.5 Angstrom resolution

Chowdhury, S.R., Sen, U.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 189.07 kDa 
• Atom Count: 13,383 
• Modeled Residue Count: 1,686 
• Deposited Residue Count: 1,728 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Intracellular protease/amidase	A, B, C, D, E, F	288	Vibrio cholerae O395	Mutation(s): 0  Gene Names: VC0395_0351, VC395_A0912 EC: 4.2.1.130
UniProt
Find proteins for A0A0H3AFW5 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A0A0H3AFW5  Go to UniProtKB:  A0A0H3AFW5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.256 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.375	α = 90
b = 80.069	β = 95.35
c = 133.133	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-15 
Deposition Author(s): Chowdhury, S.R., Sen, U.

Revision History  

• Version 1.0: 2016-06-15
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary