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

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Basic information

Entry
Database: PDB / ID: 6apw
TitleCrystal structure of Staphylococcus aureus biotin protein ligase in complex with inhibitor
ComponentsBifunctional ligase/repressor BirA
KeywordsLIGASE / Inhibitor / Antibiotic
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: 2.614 Å
AuthorsCini, D.A. / Wilce, M.C.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) 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 18, 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)38,4312
Polymers38,0161
Non-polymers4161
Water1267
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)94.454, 94.454, 130.978
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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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: 38015.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: birA, BER48_001399, 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-BTV / 4-[(4-{5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentyl}-1H-1,2,3-triazol-1-yl)methyl]benzoic acid


Mass: 415.509 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25N5O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.84 Å3/Da / Density % sol: 67.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 8000,Tris-HCl pH 7.5, glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2.614→46.76 Å / Num. obs: 18559 / % possible obs: 99.79 % / Redundancy: 26.3 % / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.013 / Net I/av σ(I): 38.43 / Net I/σ(I): 38.43
Reflection shellResolution: 2.614→2.708 Å / Redundancy: 25.8 % / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 4.37 / Num. unique obs: 1788 / CC1/2: 0.948 / Rpim(I) all: 0.1675 / % possible all: 98.51

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementResolution: 2.614→46.761 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 970 5.23 %
Rwork0.1937 --
obs0.1955 18552 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.614→46.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2613 0 29 7 2649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032695
X-RAY DIFFRACTIONf_angle_d0.5873635
X-RAY DIFFRACTIONf_dihedral_angle_d7.4581607
X-RAY DIFFRACTIONf_chiral_restr0.043393
X-RAY DIFFRACTIONf_plane_restr0.003470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6141-2.75190.33051340.27922423X-RAY DIFFRACTION99
2.7519-2.92430.27151300.25732474X-RAY DIFFRACTION100
2.9243-3.150.27561400.2472476X-RAY DIFFRACTION100
3.15-3.4670.26051440.21822467X-RAY DIFFRACTION100
3.467-3.96840.20961460.19832503X-RAY DIFFRACTION100
3.9684-4.99890.19291360.15762542X-RAY DIFFRACTION100
4.9989-46.7680.22091400.17942697X-RAY DIFFRACTION100
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)
14.88580.8479-1.50578.666-0.98336.05550.03230.17850.413-0.07590.1516-0.4846-0.2742-0.1461-0.25970.54070.20520.1070.67660.12680.622624.814724.651146.3862
22.54910.1355-1.08083.39250.42382.88070.0484-0.0690.18020.03510.17160.2354-0.3844-0.3725-0.27370.46720.01630.06060.66510.11850.418240.711713.89324.9691
32.0090.3784-0.77054.244-0.11213.18840.080.16940.3967-0.29240.27570.4246-0.6586-0.3004-0.3550.52170.00430.05870.65340.13940.511143.155121.554614.9662
45.3498-0.3327-1.78076.69920.05748.0272-0.12570.1981-0.2633-0.6012-0.1463-0.48550.28520.12860.21810.7647-0.07370.09060.71940.03420.502953.841316.7358-0.6355
58.2796-5.08522.88528.18494.15057.9352-0.29520.10210.8603-0.364-0.3199-1.6848-2.00781.84920.11260.6342-0.22580.04590.631-0.05360.738751.234218.571920.6051
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:62 )A2 - 62
2X-RAY DIFFRACTION2( CHAIN A AND RESID 63:168 )A63 - 168
3X-RAY DIFFRACTION3( CHAIN A AND RESID 169:288 )A169 - 288
4X-RAY DIFFRACTION4( CHAIN A AND RESID 289:323 )A289 - 323
5X-RAY DIFFRACTION5( CHAIN A AND RESID 401:401 )A401

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