4OVD

Crystal structure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum DSM 20469

PDB DOI: https://doi.org/10.2210/pdb4OVD/pdb

Classification: TRANSFERASE
Organism(s): Lancefieldella parvula DSM 20469
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2014-02-21 Released: 2014-03-12
Deposition Author(s): Filippova, E.V., Wawrzak, Z., Kiryukhina, O., Babnigg, G., Clancy, S., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.233
R-Value Work: 0.179
R-Value Observed: 0.182

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum DSM 20469

Filippova, E.V., Wawrzak, Z., Kiryukhina, O., Babnigg, G., Clancy, S., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 61.52 kDa
Atom Count: 3,336
Modelled Residue Count: 422
Deposited Residue Count: 564
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan glycosyltransferase	A	564	Lancefieldella parvula DSM 20469	Mutation(s): 0 Gene Names: Apar_0480 EC: 2.4.1.129
UniProt
Find proteins for C8W9X3 (Lancefieldella parvula (strain ATCC 33793 / DSM 20469 / CCUG 32760 / JCM 10300 / KCTC 3663 / VPI 0546 / 1246)) Explore C8W9X3 Go to UniProtKB: C8W9X3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C8W9X3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.233
R-Value Work: 0.179
R-Value Observed: 0.182
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.68	α = 90
b = 45.51	β = 102.78
c = 71.29	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
Aimless	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-03-12

Deposition Author(s):

Filippova, E.V.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2014-03-12
Type: Initial release
Version 1.1: 2014-08-13
Changes: Structure summary
Version 1.2: 2017-11-22
Changes: Refinement description
Version 1.3: 2018-01-24
Changes: Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.