8GKD | pdb_00008gkd

Crystal structure of the peptidoglycan O-acetylesterase Ape1 (amino acids 41-392) from Campylobacter jejuni

PDB DOI: https://doi.org/10.2210/pdb8GKD/pdb

Classification: HYDROLASE
Organism(s): Campylobacter jejuni subsp. jejuni 81-176
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-03-17 Released: 2024-03-20
Deposition Author(s): Lin, C.S., Murphy, M.E.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.188 (Depositor), 0.190 (DCC)
R-Value Work:
0.166 (Depositor), 0.170 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Mechanism of the CBM35 domain in assisting catalysis by Ape1, a Campylobacter jejuni O-acetyl esterase

Lin, C.S., Yen, I.Y., Chan, A.C., Murphy, M.E.

To be published.

Macromolecule Content

Total Structure Weight: 123.21 kDa
Atom Count: 9,133
Modeled Residue Count: 1,062
Deposited Residue Count: 1,074
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SGNH hydrolase-type esterase domain-containing protein	A, B, C	358	Campylobacter jejuni subsp. jejuni 81-176	Mutation(s): 0 Gene Names: CJJ81176_0638
UniProt
Find proteins for A0A0H3PJ52 (Campylobacter jejuni subsp. jejuni serotype O:23/36 (strain 81-176)) Explore A0A0H3PJ52 Go to UniProtKB: A0A0H3PJ52
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3PJ52
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT (Subject of Investigation/LOI) Query on ACT Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.188 (Depositor), 0.190 (DCC)
R-Value Work: 0.166 (Depositor), 0.170 (DCC)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.905	α = 90
b = 94.905	β = 90
c = 102.741	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-03-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	MOP-142176

Revision History (Full details and data files)

Version 1.0: 2024-03-20
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.