4WJM | pdb_00004wjm

Crystal structure of Fructokinase from Brucella abortus 2308 with bound AMPPNP

• PDB DOI: https://doi.org/10.2210/pdb4WJM/pdb

• Classification: TRANSFERASE
• Organism(s): Brucella abortus 2308
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-10-01 Released: 2014-10-22 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.195 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.170 (Depositor) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

Crystal structure of Fructokinase from Brucella abortus 2308 with bound AMPPNP

Horanyi, P.S., Dranow, D.M., Fischer, E., Abendroth, J., Lorimer, D.D., Edwards, T.

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: 34.38 kDa 
• Atom Count: 2,748 
• Modeled Residue Count: 312 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribokinase:Carbohydrate kinase, PfkB	A	312	Brucella abortus 2308	Mutation(s): 0  Gene Names: cscK, BAB1_0112 EC: 2.7.1.4
UniProt
Find proteins for Q2YNY7 (Brucella abortus (strain 2308)) Explore Q2YNY7  Go to UniProtKB:  Q2YNY7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MLA	F [auth A]	MALONIC ACID C3 H4 O4 OFOBLEOULBTSOW-UHFFFAOYSA-N
EDO	D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.195 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.170 (Depositor) 
• R-Value Observed: 0.171 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34WJM

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.89	α = 90
b = 109.89	β = 90
c = 58.1	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-10-22 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2014-10-22
  Type: Initial release
  
• Version 1.1: 2015-04-29
  Changes: Non-polymer description
• Version 1.2: 2017-09-06
  Changes: Author supporting evidence, Derived calculations, Other, Source and taxonomy, Structure summary
• Version 1.3: 2017-11-22
  Changes: Refinement description
• Version 1.4: 2019-12-11
  Changes: Author supporting evidence
• Version 1.5: 2023-12-27
  Changes: Data collection, Database references, Refinement description