3IF2 | pdb_00003if2

Crystal structure of Putative amino-acid aminotransferase (YP_265399.1) from Psychrobacter arcticum 273-4 at 2.50 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3IF2/pdb

• Classification: TRANSFERASE
• Organism(s): Psychrobacter arcticus 273-4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-23 Released: 2009-08-04 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.221 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Crystal structure of Putative amino-acid aminotransferase (YP_265399.1) from Psychrobacter arcticum 273-4 at 2.50 A resolution

Joint Center for Structural Genomics (JCSG)

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 Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 99.94 kDa 
• Atom Count: 7,113 
• Modeled Residue Count: 874 
• Deposited Residue Count: 888 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase	A, B	444	Psychrobacter arcticus 273-4	Mutation(s): 0  Gene Names: avtA, Psyc_2118, YP_265399.1 EC: 2.6.1
UniProt
Find proteins for Q4FPU3 (Psychrobacter arcticus (strain DSM 17307 / VKM B-2377 / 273-4)) Explore Q4FPU3  Go to UniProtKB:  Q4FPU3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A], E [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
GOL	D [auth A], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	F [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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: 2.50 Å
• R-Value Free:  0.221 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33IF2

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.813	α = 90
b = 152.813	β = 90
c = 100.614	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-04 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-08-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations