2Q6E | pdb_00002q6e

Crystal structure of glucuronate isomerase from Bacillus halodurans complexed with Zn

• PDB DOI: https://doi.org/10.2210/pdb2Q6E/pdb

• Classification: ISOMERASE
• Organism(s): Halalkalibacterium halodurans C-125
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-06-05 Released: 2007-06-19 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Patskovsky, Y., Toro, R., Sauder, J.M., Burley, S.K., Rauschel, F.M., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.246 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of glucuronate isomerase from Bacillus halodurans complexed with Zn.

Fedorov, A.A., Fedorov, E.V., Patskovsky, Y., Toro, R., Sauder, J.M., Burley, S.K., Raushel, F.M., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 150.28 kDa 
• Atom Count: 10,380 
• Modeled Residue Count: 1,236 
• Deposited Residue Count: 1,281 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BH0493 protein	A, B, C	427	Halalkalibacterium halodurans C-125	Mutation(s): 0  Gene Names: BH0493
UniProt
Find proteins for Q9KFI6 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9KFI6  Go to UniProtKB:  Q9KFI6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], F [auth B], G [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	H [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.246 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.372	α = 90
b = 133.372	β = 90
c = 196.821	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-19 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Patskovsky, Y., Toro, R., Sauder, J.M., Burley, S.K., Rauschel, F.M., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-06-19
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2023-08-30
  Changes: Data collection, Database references, Refinement description