2YWD | pdb_00002ywd

Crystal structure of glutamine amidotransferase

• PDB DOI: https://doi.org/10.2210/pdb2YWD/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-04-20 Released: 2007-10-23 
• Deposition Author(s): Manzoku, M., Ebihara, A., Yokoyama, S., Kuramitsu, 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: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of glutamine amidotransferase

Manzoku, M., Ebihara, A., Fujimoto, Y., Yokoyama, S., Kuramitsu, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.24 kDa 
• Atom Count: 1,634 
• Modeled Residue Count: 189 
• Deposited Residue Count: 191 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamine amidotransferase subunit pdxT	A	191	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: pdxT EC: 2.6 (PDB Primary Data), 4.3.3.6 (UniProt), 3.5.1.2 (UniProt)
UniProt
Find proteins for Q5SKD6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKD6  Go to UniProtKB:  Q5SKD6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.088	α = 90
b = 66.761	β = 90
c = 80.665	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-23 
Deposition Author(s): Manzoku, M., Ebihara, A., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-10-23
  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, Refinement description