4DXE | pdb_00004dxe

2.52 Angstrom resolution crystal structure of the acyl-carrier-protein synthase (AcpS)-acyl carrier protein (ACP) protein-protein complex from Staphylococcus aureus subsp. aureus COL

PDB DOI: https://doi.org/10.2210/pdb4DXE/pdb

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

Deposited: 2012-02-27 Released: 2012-03-14
Deposition Author(s): Halavaty, A.S., Minasov, G., Filippova, E.V., Dubrovska, I., Winsor, J., Shuvalova, L., Peterson, S.N., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free:
0.254 (Depositor), 0.261 (DCC)
R-Value Work:
0.200 (Depositor), 0.201 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

2.52 Angstrom resolution crystal structure of the acyl-carrier-protein synthase (AcpS)-acyl carrier protein (ACP) protein-protein complex from Staphylococcus aureus subsp. aureus COL

Halavaty, A.S., Minasov, G., Filippova, E.V., Dubrovska, I., Winsor, J., Shuvalova, L., Peterson, S.N., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 166.45 kDa
Atom Count: 9,273
Modeled Residue Count: 1,130
Deposited Residue Count: 1,464
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
acyl-carrier-protein synthase	A, B, C, D, E A, B, C, D, E, F	143	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5HED0
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl carrier protein	G [auth H] H [auth L] I [auth K] J [auth G] K [auth J] G [auth H], H [auth L], I [auth K], J [auth G], K [auth J], L [auth I]	101	Staphylococcus aureus subsp. aureus COL	Mutation(s): 0 Gene Names: acpP, apcP, SACOL1247
UniProt
Find proteins for Q5HGK0 (Staphylococcus aureus (strain COL)) Explore Q5HGK0 Go to UniProtKB: Q5HGK0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5HGK0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain P [auth F] SDF format, chain O [auth C] SDF format, chain N [auth B] SDF format, chain M [auth A] MOL2 format, chain P [auth F] MOL2 format, chain O [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth A] mmCIF format, chain P [auth F] mmCIF format, chain O [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth A]	M [auth A], N [auth B], O [auth C], P [auth F]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth F] Interactions & Density Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free: 0.254 (Depositor), 0.261 (DCC)
R-Value Work: 0.200 (Depositor), 0.201 (DCC)
R-Value Observed: 0.203 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.968	α = 90
b = 102.961	β = 115.87
c = 77.298	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-03-14

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2012-03-14
Type: Initial release
Version 1.1: 2012-03-21
Changes: Other
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description