5CXD

1.75 Angstrom resolution crystal structure of the apo-form acyl-carrier-protein synthase (AcpS) (acpS; purification tag off) from Staphylococcus aureus subsp. aureus COL in the I4 space group

PDB DOI: https://doi.org/10.2210/pdb5CXD/pdb

Classification: TRANSFERASE
Organism(s): Staphylococcus aureus subsp. aureus COL
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-07-28 Released: 2015-08-05
Deposition Author(s): Halavaty, A.S., Minasov, G., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.203
R-Value Work: 0.169
R-Value Observed: 0.170

wwPDB Validation 3D Report Full Report

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

Literature

1.75 Angstrom resolution crystal structure of the apo-form acyl-carrier-protein synthase (AcpS) (acpS; purification tag off) from Staphylococcus aureus subsp. aureus COL in the I4 space group

Halavaty, A.S., Minasov, G., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 42.29 kDa
Atom Count: 3,454
Modelled Residue Count: 362
Deposited Residue Count: 366
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Holo-[acyl-carrier-protein] synthase	A, B, C	122	Staphylococcus aureus subsp. aureus COL	Mutation(s): 0 Gene Names: acpS, SACOL2061 EC: 2.7.8.7
UniProt
Find proteins for Q5HED0 (Staphylococcus aureus (strain COL)) Explore Q5HED0 Go to UniProtKB: Q5HED0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5HED0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain Q [auth C] MOL2 format, chain Q [auth C]	Q [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain Q [auth C] Interactions & Density Focus chain Q [auth C]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C]	M [auth C]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [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 A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth B], N [auth C], O [auth C], P [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.203
R-Value Work: 0.169
R-Value Observed: 0.170
Space Group: I 4
Diffraction Data: https://doi.org/10.18430/m35cxd

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.117	α = 90
b = 103.117	β = 90
c = 71.189	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
BLU-MAX	data collection
PHASER	phasing
Coot	model building
HKL-2000	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-08-05

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2015-08-05
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description