4R0Q | pdb_00004r0q

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

PDB DOI: https://doi.org/10.2210/pdb4R0Q/pdb

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

Deposited: 2014-08-01 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: 2.00 Å
R-Value Free:
0.217 (Depositor), 0.221 (DCC)
R-Value Work:
0.179 (Depositor), 0.186 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 102.78 kDa
Atom Count: 6,398
Modeled Residue Count: 825
Deposited Residue Count: 964
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C8W8H7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CEP Query on CEP Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	CEPHALOTHIN GROUP C₁₆ H₁₈ N₂ O₆ S₂ UUWFGEKEQSCSMB-IAQYHMDHSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
B3P Query on B3P Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₁₁ H₂₆ N₂ O₆ HHKZCCWKTZRCCL-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
SCN Query on SCN Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [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: 2.00 Å
R-Value Free: 0.217 (Depositor), 0.221 (DCC)
R-Value Work: 0.179 (Depositor), 0.186 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.553	α = 90
b = 70.002	β = 96.76
c = 115.233	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

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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
Version 1.4: 2024-11-20
Changes: Structure summary