5XU7 | pdb_00005xu7

Crystal structure of Escherichia coli holo-[acyl-carrier-protein] synthase (AcpS)

PDB DOI: https://doi.org/10.2210/pdb5XU7/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-06-22 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: 1.84 Å
R-Value Free:
0.214 (Depositor), 0.216 (DCC)
R-Value Work:
0.175 (Depositor)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5XU7

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: 42.42 kDa
Atom Count: 3,231
Modeled Residue Count: 358
Deposited Residue Count: 378
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Holo-[acyl-carrier-protein] synthase	A, B, C	126	Escherichia coli K-12	Mutation(s): 0 Gene Names: acpS, dpj, b2563, JW2547 EC: 2.7.8.7
UniProt
Find proteins for P24224 (Escherichia coli (strain K12)) Explore P24224 Go to UniProtKB: P24224
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24224
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth C] MOL2 format, chain G [auth C] mmCIF format, chain G [auth C]	G [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Interactions & Density Focus chain G [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth C]	D [auth A], E [auth A], F [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.214 (Depositor), 0.216 (DCC)
R-Value Work: 0.175 (Depositor)
R-Value Observed: 0.177 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.62	α = 90
b = 97.62	β = 90
c = 96.14	γ = 90

Software Package:

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

Structure Validation

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.