4MSO | pdb_00004mso

X-ray crystal structure of a serine hydroxymethyl transferase in apo form from Burkholderia cenocepacia

• PDB DOI: https://doi.org/10.2210/pdb4MSO/pdb

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


• Deposited: 2013-09-18 Released: 2013-12-11 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.182 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.146 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

Literature

X-ray crystal structure of a serine hydroxymethyl transferase in apo form from Burkholderia cenocepacia

Fairman, J.W., Jensen, M.M., Sullivan, A.H., Abendroth, J., 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 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 92.31 kDa 
• Atom Count: 6,803 
• Modeled Residue Count: 765 
• Deposited Residue Count: 846 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase	A, B	423	Burkholderia cenocepacia J2315	Mutation(s): 0  Gene Names: glyA, glyA1, BceJ2315_31420, 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth A], F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	E [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.182 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.146 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34MSO

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.28	α = 90
b = 72.58	β = 90
c = 182.12	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-11 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2013-12-11
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description