4OTL | pdb_00004otl

X-ray Crystal Structure of Serine Hydroxymethyl Transferase from Burkholderia cenocepacia bound to PLP and Glycine

• PDB DOI: https://doi.org/10.2210/pdb4OTL/pdb

• Classification: TRANSFERASE
• Organism(s): Burkholderia cenocepacia J2315
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-02-13 Released: 2014-04-23 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.224 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

X-ray Crystal Structure of Serine Hydroxymethyl Transferase from Burkholderia cenocepacia bound to PLP and Glycine

Fairman, J.W., Jensen, M.M., Sullivan, A.H., Edwards, T.E., Lorimer, D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 185.28 kDa 
• Atom Count: 13,382 
• Modeled Residue Count: 1,648 
• Deposited Residue Count: 1,692 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase	A, B, C, D	423	Burkholderia cenocepacia J2315	Mutation(s): 0  Gene Names: glyA, BCAL3197 EC: 2.1.2.1
UniProt
Find proteins for B4ECY9 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4ECY9  Go to UniProtKB:  B4ECY9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	E [auth A], G [auth B], J [auth C], L [auth D]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
GLY	F [auth A], H [auth B], K [auth C], M [auth D]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
EDO	I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.224 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34OTL

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.97	α = 90
b = 179.69	β = 115.43
c = 75.51	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-23 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2014-04-23
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description