4XCK | pdb_00004xck

Vibrio cholerae O395 Ribokinase complexed with ADP, Ribose and Cesium ion.

• PDB DOI: https://doi.org/10.2210/pdb4XCK/pdb

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


• Deposited: 2014-12-18 Released: 2015-01-21 
• Deposition Author(s): Paul, R., Patra, M.D., Sen, U.
• Funding Organization(s): DEPARTMENT OF ATOMIC ENERGY, DEPARTMENT OF BIOTECHNOLOGY

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 
  0.251 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Apo and Ligand Bound Vibrio cholerae Ribokinase (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)

Macromolecule Content

• Total Structure Weight: 132.54 kDa 
• Atom Count: 9,407 
• Modelled Residue Count: 1,224 
• Deposited Residue Count: 1,236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribokinase	A, B, C, D	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	F [auth A], H [auth B], I [auth B], L [auth C], N [auth D]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
RIB	E [auth A], K [auth C]	alpha-D-ribofuranose C5 H10 O5 HMFHBZSHGGEWLO-AIHAYLRMSA-N
CS	G [auth A], J [auth B], M [auth C], O [auth D]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free:  0.251 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.304	α = 106.99
b = 69.553	β = 98.77
c = 78.316	γ = 96.46

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, DEPARTMENT OF BIOTECHNOLOGY	India	--

Revision History  

• Version 1.0: 2015-01-21
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Data collection, Derived calculations, Source and taxonomy, Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary