6XDK | pdb_00006xdk

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

• PDB DOI: https://doi.org/10.2210/pdb6XDK/pdb

• Classification: TRANSFERASE
• Organism(s): Stenotrophomonas maltophilia K279a
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2020-06-10 Released: 2020-06-24 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.181 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

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.

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

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: 161.4 kDa 
• Atom Count: 13,450 
• Modeled Residue Count: 1,427 
• Deposited Residue Count: 1,476 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoserine aminotransferase	A, B, C, D	369	Stenotrophomonas maltophilia K279a	Mutation(s): 0  Gene Names: serC, Smlt3098 EC: 2.6.1.52
UniProt
Find proteins for B2FKF0 (Stenotrophomonas maltophilia (strain K279a)) Explore B2FKF0  Go to UniProtKB:  B2FKF0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP (Subject of Investigation/LOI)	J [auth B], N [auth C]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
EDO	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	G [auth B], K [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	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 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36xdk

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.35	α = 84.985
b = 71.62	β = 88.816
c = 89.86	γ = 63.369

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
MoRDa	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-24 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

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