2PBY | pdb_00002pby

Probable Glutaminase from Geobacillus kaustophilus HTA426

• PDB DOI: https://doi.org/10.2210/pdb2PBY/pdb

• Classification: HYDROLASE
• Organism(s): Geobacillus kaustophilus HTA426
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-03-29 Released: 2007-06-12 
• Deposition Author(s): Dillard, B.D., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S., Rose, J.P., Wang, B.-C., RIKEN Structural Genomics/Proteomics Initiative (RSGI), Southeast Collaboratory for Structural Genomics (SECSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 
  0.249 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.195 (Depositor) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Glutaminase from Geobacillus kaustophilus HTA426

Dillard, B.D., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S., Rose, J.P., Wang, B.-C.

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 135.24 kDa 
• Atom Count: 9,310 
• Modeled Residue Count: 1,155 
• Deposited Residue Count: 1,232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutaminase	A, B, C, D	308	Geobacillus kaustophilus HTA426	Mutation(s): 0  Gene Names: GK2125 EC: 3.5.1.2
UniProt
Find proteins for Q5KY26 (Geobacillus kaustophilus (strain HTA426)) Explore Q5KY26  Go to UniProtKB:  Q5KY26

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free:  0.249 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.195 (Depositor) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.503	α = 90
b = 86.786	β = 109.76
c = 106.881	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-12 
Deposition Author(s): Dillard, B.D., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S., Rose, J.P., Wang, B.-C., RIKEN Structural Genomics/Proteomics Initiative (RSGI), Southeast Collaboratory for Structural Genomics (SECSG)

Revision History  

• Version 1.0: 2007-06-12
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.5: 2023-08-30
  Changes: Data collection, Database references, Refinement description