4X8F

Vibrio cholerae O395 Ribokinase in apo form

• PDB DOI: https://doi.org/10.2210/pdb4X8F/pdb

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


• Deposited: 2014-12-10 Released: 2015-01-21 
• Deposition Author(s): Paul, R., Patra, M.D., Sen, U.
• Funding Organization(s): Department of Atomic Energy, ,Govt. of India, Department of Biotechnology, Govt. of India

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.308 
• R-Value Work: 0.239 
• R-Value Observed: 0.242 

Starting Model: experimental

Literature

Crystal Structure of Apo and Ligand Bound Vibrio choleraeRibokinase (Vc-RK): Role of Monovalent Cation Induced Activation and Structural Flexibility in Sugar Phosphorylation

Paul, R., Patra, M.D., Sen, U.

(2015) Adv Exp Med Biol 842: 293-307

• PubMed: 25408351 
• DOI: https://doi.org/10.1007/978-3-319-11280-0_19
• Primary Citation of Related Structures:  
  4X8F, 4XCK, 4XDA

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Organizational Affiliation: 

Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF Bidhan Nagar, WB, Kolkata, 700 064, India.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 assigned by authors and generated by PISA (software)

Biological Assembly 7  

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

Biological assembly 7 assigned by authors and generated by PISA (software)

Biological Assembly 8  

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

Biological assembly 8 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 518.28 kDa 
• Atom Count: 36,000 
• Modelled Residue Count: 4,896 
• Deposited Residue Count: 4,944 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribokinase	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	309	Vibrio cholerae O395	Mutation(s): 0  Gene Names: rbsK, VC0395_0007, VC395_A0124 EC: 2.7.1.15
UniProt
Find proteins for A0A0H2UL04 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A0A0H2UL04  Go to UniProtKB:  A0A0H2UL04

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.308 
• R-Value Work: 0.239 
• R-Value Observed: 0.242 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.22	α = 110.52
b = 130.849	β = 90
c = 145.69	γ = 119.59

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-01-21 
Deposition Author(s): Paul, R., Patra, M.D., Sen, U.

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Funding Organization	Location	Grant Number
Department of Atomic Energy, ,Govt. of India	India	--
Department of Biotechnology, Govt. of India	India	--

Revision History  

• Version 1.0: 2015-01-21
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Data collection, Derived calculations, Source and taxonomy
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description