4MSO

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.182
R-Value Work: 0.146
R-Value Observed: 0.148

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B4ECY9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	C [auth A], D [auth A], F [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B]	E [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.182
R-Value Work: 0.146
R-Value Observed: 0.148
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/M34MSO

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-12-11

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

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

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Deposit Data

Help and Resources

4MSO

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)