4OVD | pdb_00004ovd

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.233 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

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: 61.52 kDa 
• Atom Count: 3,336 
• Modeled Residue Count: 422 
• Deposited Residue Count: 564 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE	A	MET	Selenomethionine	C5 H11 N O2 Se

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.233 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

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

Entry History 

Deposition Data

• Released Date: 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)

Revision History  

• 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
• Version 1.4: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary