4R23 | pdb_00004r23

Structure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with dicloxacillin

• PDB DOI: https://doi.org/10.2210/pdb4R23/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Lancefieldella parvula DSM 20469
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-08-08 Released: 2014-09-17 
• Deposition Author(s): Filippova, E.V., Minasov, G., Kiryukhina, O., 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: 1.84 Å
• R-Value Free: 
  0.192 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Structure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with dicloxacillin

Filippova, E.V., Minasov, G., Kiryukhina, O., Clancy, S., Joachimiak, A., Anderson, W.F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 103.21 kDa 
• Atom Count: 6,490 
• Modeled Residue Count: 827 
• Deposited Residue Count: 964 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan glycosyltransferase	A, B	482	Lancefieldella parvula DSM 20469	Mutation(s): 0  Gene Names: Apar_1344 EC: 2.4.1.129
UniProt
Find proteins for C8W8H7 (Lancefieldella parvula (strain ATCC 33793 / DSM 20469 / CCUG 32760 / JCM 10300 / KCTC 3663 / VPI 0546 / 1246)) Explore C8W8H7  Go to UniProtKB:  C8W8H7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DXU	C [auth A], J [auth B]	Dicloxacillin, open form C19 H25 Cl2 N3 O5 S AXRWQAUUTZEPPM-YSIYDJFASA-N
P4G	D [auth A], E [auth A], F [auth A], K [auth B]	1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE C8 H18 O3 RRQYJINTUHWNHW-UHFFFAOYSA-N
EDO	G [auth A], H [auth A], I [auth A], L [auth B], M [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.192 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.611	α = 90
b = 69.882	β = 96.87
c = 114.251	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-17 
Deposition Author(s): Filippova, E.V., Minasov, G., Kiryukhina, O., Clancy, S., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2014-09-17
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 1.3: 2023-12-06
  Changes: Data collection
• Version 1.4: 2024-10-30
  Changes: Structure summary
• Version 1.5: 2025-05-28
  Changes: Derived calculations, Structure summary