3I4J | pdb_00003i4j

Crystal structure of Aminotransferase, class III from Deinococcus radiodurans

• PDB DOI: https://doi.org/10.2210/pdb3I4J/pdb

• Classification: TRANSFERASE
• Organism(s): Deinococcus radiodurans
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-07-01 Released: 2009-07-14 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Toro, R., Sauder, J.M., 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: 1.70 Å
• R-Value Free: 
  0.239 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Literature

Crystal structure of Aminotransferase, class III from Deinococcus radiodurans

Fedorov, A.A., Fedorov, E.V., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C.

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 (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 179.88 kDa 
• Atom Count: 11,873 
• Modeled Residue Count: 1,530 
• Deposited Residue Count: 1,720 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase, class III	A, B, C, D	430	Deinococcus radiodurans	Mutation(s): 1  Gene Names: DR_A0121
UniProt
Find proteins for Q9RZ32 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RZ32  Go to UniProtKB:  Q9RZ32

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth B], G [auth C], H [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.239 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.746	α = 90
b = 193.124	β = 105.41
c = 64.769	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-14 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-07-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-10-24
  Changes: Structure summary
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2021-10-13
  Changes: Database references
• Version 1.6: 2024-02-21
  Changes: Data collection