6XDK

Crystal structure of Phosphoserine aminotransferase (SerC) from Stenotrophomonas maltophilia K279a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of Phosphoserine aminotransferase (SerC) from Stenotrophomonas maltophilia K279a

Abendroth, J.Horanyi, P.S.Lorimer, D.D.Edwards, T.E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoserine aminotransferase
A, B, C, D
369Stenotrophomonas maltophilia K279aMutation(s): 0 
Gene Names: serCSmlt3098
EC: 2.6.1.52
UniProt
Find proteins for B2FKF0 (Stenotrophomonas maltophilia (strain K279a))
Explore B2FKF0 
Go to UniProtKB:  B2FKF0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2FKF0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLP (Subject of Investigation/LOI)
Query on PLP

Download Ideal Coordinates CCD File 
J [auth B],
N [auth C]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
I [auth B],
L [auth C],
M [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth B],
K [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A],
O [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.156 
  • Space Group: P 1
  • Diffraction Data: https://doi.org/10.18430/m36xdk
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.35α = 84.985
b = 71.62β = 88.816
c = 89.86γ = 63.369
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
MoRDaphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Derived calculations, Refinement description