3KE3

Crystal structure of Putative serine-pyruvate aminotransferase (YP_263484.1) from PSYCHROBACTER ARCTICUM 273-4 at 2.20 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3KE3/pdb

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


• Deposited: 2009-10-23 Released: 2009-11-03 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.210 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 

Literature

Crystal structure of Putative serine-pyruvate aminotransferase (YP_263484.1) from PSYCHROBACTER ARCTICUM 273-4 at 2.20 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: 42.84 kDa 
• Atom Count: 3,113 
• Modelled Residue Count: 371 
• Deposited Residue Count: 379 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative serine-pyruvate aminotransferase	A	379	Psychrobacter arcticus 273-4	Mutation(s): 0  Gene Names: agxT, Psyc_0177
UniProt
Find proteins for Q4FVA8 (Psychrobacter arcticus (strain DSM 17307 / VKM B-2377 / 273-4)) Explore Q4FVA8  Go to UniProtKB:  Q4FVA8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	J [auth A], K [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.210 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 
• Space Group: C 2 2 2₁
• Diffraction Data: https://doi.org/10.18430/M33KE3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.645	α = 90
b = 98.352	β = 90
c = 121.072	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-03 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-11-03
  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: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations