2ISM

Crystal structure of the putative oxidoreductase (glucose dehydrogenase) (TTHA0570) from thermus theromophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb2ISM/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-10-18 Released: 2007-11-13 
• Deposition Author(s): Jeyakanthan, J., Kanaujia, S.P., Vasuki Ranjani, C., Sekar, K., Ebihara, A., Shinkai, A., Nakagawa, N., Shimizu, N., Yamamoto, M., Kuramitsu, S., Shiro, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.208 
• R-Value Work: 0.181 
• R-Value Observed: 0.181 

Starting Model: experimental

Literature

Crystal Structure of the Putative Oxidoreductase (Glucose Dehydrogenase) (TTHA0570) from Thermus Theromophilus HB8

Jeyakanthan, J., Kanaujia, S.P., Vasuki Ranjani, C., Sekar, K., Ebihara, A., Shinkai, A., Nakagawa, N., Shimizu, N., Yamamoto, M., Kuramitsu, S., Shiro, Y., 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.

Macromolecule Content

• Total Structure Weight: 77.91 kDa 
• Atom Count: 5,815 
• Modelled Residue Count: 660 
• Deposited Residue Count: 704 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative oxidoreductase	A, B	352	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SKS3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKS3  Go to UniProtKB:  Q5SKS3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.208 
• R-Value Work: 0.181 
• R-Value Observed: 0.181 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.898	α = 90
b = 132.964	β = 97.18
c = 60.78	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-13 
Deposition Author(s): Jeyakanthan, J., Kanaujia, S.P., Vasuki Ranjani, C., Sekar, K., Ebihara, A., Shinkai, A., Nakagawa, N., Shimizu, N., Yamamoto, M., Kuramitsu, S., Shiro, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-11-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description