5EYN

Crystal structure of Fructokinase from Vibrio cholerae O395 in fructose, ADP, Beryllium trifluoride and calcium ion bound form

• PDB DOI: https://doi.org/10.2210/pdb5EYN/pdb

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


• Deposited: 2015-11-25 Released: 2016-11-30 
• Deposition Author(s): Paul, R., Nath, S., Sen, U.
• Funding Organization(s): Department of Atomic Energy

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 0.169 
• R-Value Work: 0.141 
• R-Value Observed: 0.142 

Literature

Crystal structure of Fructokinase from Vibrio cholerae O395 in apo form

Paul, R., Nath, S., Sen, U.

To be published.

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)

Macromolecule Content

• Total Structure Weight: 35.73 kDa 
• Atom Count: 2,749 
• Modelled Residue Count: 306 
• Deposited Residue Count: 323 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructokinase	A	323	Vibrio cholerae O395	Mutation(s): 0  Gene Names: cscK, VC0395_0600 EC: 2.7.1.4
UniProt
Find proteins for A0A0H3AER7 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A0A0H3AER7  Go to UniProtKB:  A0A0H3AER7

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	E [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
FRU	B [auth A]	beta-D-fructofuranose C6 H12 O6 RFSUNEUAIZKAJO-ARQDHWQXSA-N
BEF	D [auth A]	BERYLLIUM TRIFLUORIDE ION Be F3 OGIAHMCCNXDTIE-UHFFFAOYSA-K
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 0.169 
• R-Value Work: 0.141 
• R-Value Observed: 0.142 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.3	α = 90
b = 107.218	β = 90
c = 41.618	γ = 90

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: 2016-11-30 
Deposition Author(s): Paul, R., Nath, S., Sen, U.

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Funding Organization	Location	Grant Number
Department of Atomic Energy	India	--

Revision History  

• Version 1.0: 2016-11-30
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary