2QCV

CRYSTAL STRUCTURE OF a putative 5-dehydro-2-deoxygluconokinase (IOLC) FROM BACILLUS HALODURANS C-125 AT 1.90 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb2QCV/pdb

• Classification: TRANSFERASE
• Organism(s): Halalkalibacterium halodurans C-125
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-06-19 Released: 2007-08-07 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.196 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 

Literature

Crystal structure of a putative 5-dehydro-2-deoxygluconokinase (NP_243185.1) from Bacillus halodurans at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 37.32 kDa 
• Atom Count: 2,876 
• Modelled Residue Count: 325 
• Deposited Residue Count: 332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative 5-dehydro-2-deoxygluconokinase	A	332	Halalkalibacterium halodurans C-125	Mutation(s): 6  Gene Names: NP_243185.1, iolC, BH2319 EC: 2.7.1.92
UniProt
Find proteins for Q9KAG8 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9KAG8  Go to UniProtKB:  Q9KAG8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	B [auth A], C [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.196 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 
• Space Group: P 6₄ 2 2
• Diffraction Data: https://doi.org/10.18430/M32QCV

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 194.001	α = 90
b = 194.001	β = 90
c = 48.083	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-07 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-08-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-18
  Changes: Refinement description
• Version 1.3: 2017-10-25
  Changes: Author supporting evidence
• Version 1.4: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.5: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.6: 2024-11-13
  Changes: Data collection, Structure summary