4R1G

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

PDB DOI: https://doi.org/10.2210/pdb4R1G/pdb

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

Deposited: 2014-08-05 Released: 2014-08-27
Deposition Author(s): Filippova, E.V., Minasov, G., Kiryukhina, O., Clancy, S., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.206
R-Value Work: 0.170
R-Value Observed: 0.172

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 102.17 kDa
Atom Count: 6,541
Modelled Residue Count: 836
Deposited Residue Count: 964
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C8W8H7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CXU Query on CXU Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	CLOXACILLIN (OPEN FORM) C₁₉ H₂₀ Cl N₃ O₅ S DMRXQBXKFQMOBD-ISTRZQFTSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.206
R-Value Work: 0.170
R-Value Observed: 0.172
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.52	α = 90
b = 69.889	β = 97.08
c = 114.304	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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-08-27

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2014-08-27
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
Version 1.3: 2023-12-06
Changes: Data collection

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4R1G

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)