4HA8 | pdb_00004ha8

Structure of Staphylococcus aureus biotin protein ligase in complex with biotin acetylene

PDB DOI: https://doi.org/10.2210/pdb4HA8/pdb

Classification: LIGASE
Organism(s): Staphylococcus aureus subsp. aureus ECT-R 2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-09-25 Released: 2013-10-30
Deposition Author(s): Yap, M., Wilce, M., Polyak, S, Soares da Costa, T., Tieu, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.236 (Depositor), 0.228 (DCC)
R-Value Work:
0.197 (Depositor), 0.190 (DCC)
R-Value Observed:
0.199 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Structure of Staphylococcus aureus biotin protein ligase in complex with biotin acetylene

Yap, M., Wilce, M., Polyak, S, Soares da Costa, T., Tieu, W.

To be published.

Macromolecule Content

Total Structure Weight: 38.11 kDa
Atom Count: 2,774
Modeled Residue Count: 322
Deposited Residue Count: 328
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Biotin-[acetyl-CoA-carboxylase] ligase	A	328	Staphylococcus aureus subsp. aureus ECT-R 2	Mutation(s): 0 Gene Names: ECTR2_1310 EC: 6.3.4.15
UniProt
Find proteins for A0A0H3JRH8 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore A0A0H3JRH8 Go to UniProtKB: A0A0H3JRH8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3JRH8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BC4 Query on BC4 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]	(3aS,4S,6aR)-4-(hex-5-yn-1-yl)tetrahydro-1H-thieno[3,4-d]imidazol-2(3H)-one C₁₁ H₁₆ N₂ O S MGFIEEWTLUFGHD-GUBZILKMSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.236 (Depositor), 0.228 (DCC)
R-Value Work: 0.197 (Depositor), 0.190 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.02	α = 90
b = 93.02	β = 90
c = 129.94	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-10-30

Deposition Author(s):

Soares da Costa, T.

Revision History (Full details and data files)

Version 1.0: 2013-10-30
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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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.