2CB0

Crystal structure of glucosamine 6-phosphate deaminase from Pyrococcus furiosus

• PDB DOI: https://doi.org/10.2210/pdb2CB0/pdb

• Classification: ISOMERASE
• Organism(s): Pyrococcus furiosus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2005-12-23 Released: 2007-03-13 
• Deposition Author(s): Kim, K.J., Kim, M.H., Kang, B.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.219 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Literature

The Crystal Structure of a Novel Glucosamine-6-Phosphate Deaminase from the Hyperthermophilic Archaeon Pyrococcus Furiosus

Kim, K.J., Kim, M.H., Kim, G., Kang, B.S.

(2007) Proteins 68: 413

• PubMed: 17387737 
• DOI: https://doi.org/10.1002/prot.21322
• Primary Citation of Related Structures:  
  2CB0

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Organizational Affiliation: 

Pohang Accelerator Laboratory, POSTECH, Pohang 790-784, Korea.

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 (software)

Macromolecule Content

• Total Structure Weight: 76.45 kDa 
• Atom Count: 5,513 
• Modelled Residue Count: 653 
• Deposited Residue Count: 666 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUCOSAMINE-FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE	A, B	333	Pyrococcus furiosus	Mutation(s): 0
UniProt
Find proteins for Q8U3U3 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U3U3  Go to UniProtKB:  Q8U3U3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.219 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.48	α = 90
b = 93.89	β = 90
c = 200.65	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-13 
Deposition Author(s): Kim, K.J., Kim, M.H., Kang, B.S.

Revision History  

• Version 1.0: 2007-03-13
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary