5XUK | pdb_00005xuk

Crystal structure of Helicobacter pylori holo-[acyl-carrier-protein] synthase (AcpS) in complex with coenzyme A

PDB DOI: https://doi.org/10.2210/pdb5XUK/pdb

Classification: TRANSFERASE
Organism(s): Helicobacter pylori 26695
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-06-23 Released: 2018-06-27
Deposition Author(s): Liao, Y.P., Wang, D.L., Yin, D.P., Zhang, Q.Y., Wang, Y.M., Wang, D.Q., Zhu, H.X., Chen, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.277 (Depositor), 0.280 (DCC)
R-Value Work:
0.228 (Depositor), 0.230 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structures of acyl carrier protein synthases (AcpS) from three Gram-negative bacteria

Liao, Y.P., Wang, D.L., Yin, D.P., Zhang, Q.Y., Wang, Y.M., Wang, D.Q., Zhu, H.X., Chen, S.

To be published.

Macromolecule Content

Total Structure Weight: 13.79 kDa
Atom Count: 948
Modeled Residue Count: 115
Deposited Residue Count: 119
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Holo-[acyl-carrier-protein] synthase	A	119	Helicobacter pylori 26695	Mutation(s): 0 Gene Names: acpS, HP_0808 EC: 2.7.8.7
UniProt
Find proteins for O25488 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25488 Go to UniProtKB: O25488
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O25488
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.277 (Depositor), 0.280 (DCC)
R-Value Work: 0.228 (Depositor), 0.230 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.34	α = 90
b = 93.34	β = 90
c = 43.02	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-06-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-06-27
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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.