5XUM | pdb_00005xum

Crystal structure of Thermotoga maritima holo-[acyl-carrier-protein] synthase (AcpS)

PDB DOI: https://doi.org/10.2210/pdb5XUM/pdb

Classification: TRANSFERASE
Organism(s): Thermotoga maritima MSB8
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: 2.10 Å
R-Value Free:
0.221 (Depositor), 0.233 (DCC)
R-Value Work:
0.169 (Depositor)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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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: 19.41 kDa
Atom Count: 1,427
Modeled Residue Count: 168
Deposited Residue Count: 169
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	169	Thermotoga maritima MSB8	Mutation(s): 0 Gene Names: acpS, TM_0692 EC: 2.7.8.7
UniProt
Find proteins for Q9WZF6 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZF6 Go to UniProtKB: Q9WZF6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WZF6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.221 (Depositor), 0.233 (DCC)
R-Value Work: 0.169 (Depositor)
R-Value Observed: 0.172 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.96	α = 90
b = 72.96	β = 90
c = 84.22	γ = 120

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.