3MDN

Structure of glutamine aminotransferase class-II domain protein (SPO2029) from silicibacter pomeroyi

• PDB DOI: https://doi.org/10.2210/pdb3MDN/pdb

• Classification: TRANSFERASE
• Organism(s): Ruegeria pomeroyi
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-03-30 Released: 2010-05-12 
• Deposition Author(s): Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.253 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Literature

Structure of glutamine aminotransferase class-II domain protein (SPO2029) from silicibacter pomeroyi

Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.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: 122.4 kDa 
• Atom Count: 6,847 
• Modelled Residue Count: 871 
• Deposited Residue Count: 1,096 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamine aminotransferase class-II domain protein	A, B, C, D	274	Ruegeria pomeroyi	Mutation(s): 0  Gene Names: SPO2029
UniProt
Find proteins for Q5LRU5 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LRU5  Go to UniProtKB:  Q5LRU5

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.253 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.367	α = 90
b = 72.96	β = 91.77
c = 106.722	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
PHENIX	phasing
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-12 
Deposition Author(s): Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-05-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary