2YR1 | pdb_00002yr1

Crystal Structure of 3-dehydroquinate dehydratase from Geobacillus kaustophilus HTA426

• PDB DOI: https://doi.org/10.2210/pdb2YR1/pdb

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


• Deposited: 2007-04-01 Released: 2007-10-02 
• Deposition Author(s): Kagawa, W., Kurumizaka, H., Bessho, Y., Chen, L., Fu, Z.Q., Chrzas, J., Wang, B.C., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.292 (Depositor), 0.291 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of 3-dehydroquinate dehydratase from Geobacillus kaustophilus HTA426

Kagawa, W., Kurumizaka, H., Bessho, Y., Chen, L., Fu, Z.Q., Chrzas, J., Wang, B.C., Yokoyama, S.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 57.19 kDa 
• Atom Count: 4,177 
• Modeled Residue Count: 514 
• Deposited Residue Count: 514 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-dehydroquinate dehydratase	A, B	257	Geobacillus kaustophilus HTA426	Mutation(s): 0  EC: 4.2.1.10
UniProt
Find proteins for Q5KY94 (Geobacillus kaustophilus (strain HTA426)) Explore Q5KY94  Go to UniProtKB:  Q5KY94

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.292 (Depositor), 0.291 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.309	α = 90
b = 76.642	β = 90
c = 86.571	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-02 
Deposition Author(s): Kagawa, W., Kurumizaka, H., Bessho, Y., Chen, L., Fu, Z.Q., Chrzas, J., Wang, B.C., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-10-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Refinement description