4JBF

Crystal structure of peptidoglycan glycosyltransferase from Atopobium parvulum DSM 20469.

PDB DOI: https://doi.org/10.2210/pdb4JBF/pdb

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

Deposited: 2013-02-19 Released: 2013-03-20
Deposition Author(s): Filippova, E.V., Wawrzak, Z., Minasov, G., Shuvalova, L., Kiryukhina, O., Babnigg, G., Rubin, E., Sacchettini, J., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG), Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.237
R-Value Work: 0.195
R-Value Observed: 0.197

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of peptidoglycan glycosyltransferase from Atopobium parvulum DSM 20469.

Filippova, E.V., Wawrzak, Z., Minasov, G., Shuvalova, L., Kiryukhina, O., Babnigg, G., Rubin, E., Sacchettini, J., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG), Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

To be published.

Macromolecule Content

Total Structure Weight: 101.49 kDa
Atom Count: 6,378
Modelled Residue Count: 820
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
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [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: 0.237
R-Value Work: 0.195
R-Value Observed: 0.197
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M34JBF

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.927	α = 90
b = 70.167	β = 97.35
c = 114.82	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-03-20

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

Revision History (Full details and data files)

Version 1.0: 2013-03-20
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2018-01-24
Changes: Database references, Structure summary
Version 1.3: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary

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4JBF

Crystal structure of peptidoglycan glycosyltransferase from Atopobium parvulum DSM 20469.

Crystal structure of peptidoglycan glycosyltransferase from Atopobium parvulum DSM 20469.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)