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- PDB-6aqq: Crystal structure of Staphylococcus aureus biotin protein ligase ... -

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Basic information

Entry
Database: PDB / ID: 6aqq
TitleCrystal structure of Staphylococcus aureus biotin protein ligase in complex with inhibitor
ComponentsBifunctional ligase/repressor BirA
KeywordsLIGASE / Antibiotic / inhibitor
Function / homology
Function and homology information


Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.71 Å
AuthorsCini, D.A. / Wilce, M.C.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1068885 Australia
CitationJournal: ACS Infect Dis / Year: 2018
Title: Halogenation of Biotin Protein Ligase Inhibitors Improves Whole Cell Activity against Staphylococcus aureus.
Authors: Paparella, A.S. / Lee, K.J. / Hayes, A.J. / Feng, J. / Feng, Z. / Cini, D. / Deshmukh, S. / Booker, G.W. / Wilce, M.C.J. / Polyak, S.W. / Abell, A.D.
History
DepositionAug 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional ligase/repressor BirA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4042
Polymers38,0151
Non-polymers3891
Water37821
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.600, 93.600, 130.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-517-

HOH

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Components

#1: Protein Bifunctional ligase/repressor BirA / Biotin--[acetyl-CoA-carboxylase] ligase / Biotin--protein ligase / Biotin-[acetyl-CoA carboxylase] synthetase


Mass: 38014.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: birA, BO217_2143, SAMEA2236422_00088, SAMEA2236459_00088, SAMEA2384800_00088, SAMEA2384856_00382, SAMEA2445640_00088
Production host: Escherichia coli (E. coli)
References: UniProt: A0A181HT70, biotin-[biotin carboxyl-carrier protein] ligase
#2: Chemical ChemComp-BVY / (3aS,4S,6aR)-4-(5-{1-[(3-fluorophenyl)methyl]-1H-1,2,3-triazol-4-yl}pentyl)tetrahydro-1H-thieno[3,4-d]imidazol-2(3H)-one


Mass: 389.490 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24FN5OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.77 Å3/Da / Density % sol: 67.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 12% PEG 8000, 100 mM Tris-HCl pH 7.5 and 10% glycerol

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.71→41.859 Å / Num. obs: 15757 / % possible obs: 95.97 % / Redundancy: 3.7 % / Net I/σ(I): 11.08

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementResolution: 2.71→41.859 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2441 788 5 %
Rwork0.218 --
obs0.2194 15754 96.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.71→41.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2573 0 27 21 2621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052650
X-RAY DIFFRACTIONf_angle_d0.8723573
X-RAY DIFFRACTIONf_dihedral_angle_d6.6161581
X-RAY DIFFRACTIONf_chiral_restr0.047389
X-RAY DIFFRACTIONf_plane_restr0.004461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.87980.42131310.332502X-RAY DIFFRACTION99
2.8798-3.10210.28211320.27082497X-RAY DIFFRACTION98
3.1021-3.41410.26291310.23552489X-RAY DIFFRACTION98
3.4141-3.90780.22511300.20342481X-RAY DIFFRACTION96
3.9078-4.92220.191310.18172488X-RAY DIFFRACTION95
4.9222-41.86420.25381330.21692509X-RAY DIFFRACTION91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.981.81491.9763.99762.67213.5510.17870.169-0.36240.1760.1262-0.5227-0.11180.3456-0.28420.6108-0.15250.1070.6022-0.12410.649225.0348-26.121245.2811
22.397-0.3913-0.65582.40521.18533.8050.22990.13730.3044-0.18940.165-0.354-0.34740.7078-0.33090.5265-0.05240.11260.4303-0.04550.43617.6678-43.147716.3356
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 68 )
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 323 )

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