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- PDB-3v8j: Crystal structure of Staphylococcus aureus biotin protein ligase -

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Basic information

Entry
Database: PDB / ID: 3v8j
TitleCrystal structure of Staphylococcus aureus biotin protein ligase
ComponentsBiotin ligase
KeywordsLIGASE / biotin / metabolism / biotin carboxyl carrier protein
Function / homology
Function and homology information


SH3 type barrels. - #100 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / SH3 type barrels. / Arc Repressor Mutant, subunit A / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta ...SH3 type barrels. - #100 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / SH3 type barrels. / Arc Repressor Mutant, subunit A / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsPendini, N.R. / Yap, M.Y.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Selective inhibition of biotin protein ligase from Staphylococcus aureus.
Authors: Soares da Costa, T.P. / Tieu, W. / Yap, M.Y. / Pendini, N.R. / Polyak, S.W. / Sejer Pedersen, D. / Morona, R. / Turnidge, J.D. / Wallace, J.C. / Wilce, M.C. / Booker, G.W. / Abell, A.D.
History
DepositionDec 23, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Biotin ligase


Theoretical massNumber of molelcules
Total (without water)38,0151
Polymers38,0151
Non-polymers00
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.132, 51.401, 67.584
Angle α, β, γ (deg.)90.00, 108.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Biotin ligase


Mass: 38014.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: A9781 / Gene: SAOG_00031 / Production host: Escherichia coli (E. coli) / References: UniProt: C8N5A9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 8000, 10% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1.51 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.51 Å / Relative weight: 1
ReflectionResolution: 2.1→34.96 Å

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Processing

SoftwareName: PHENIX / Version: phenix.refine: 1.8_1069 / Classification: refinement
RefinementResolution: 2.1→34.956 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.36 / σ(F): 1.38 / Phase error: 27.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2574 938 5.06 %
Rwork0.1985 17596 -
obs0.2015 18534 96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.54 Å2 / Biso mean: 16.7719 Å2 / Biso min: 0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2462 0 0 204 2666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082506
X-RAY DIFFRACTIONf_angle_d1.1823380
X-RAY DIFFRACTIONf_chiral_restr0.08374
X-RAY DIFFRACTIONf_plane_restr0.004436
X-RAY DIFFRACTIONf_dihedral_angle_d17.11924
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1001-2.21080.37481410.27132470261196
2.2108-2.34920.29331220.27682491261395
2.3492-2.53060.31011320.22562474260696
2.5306-2.78510.28891330.22222526265996
2.7851-3.18790.25011240.19922541266597
3.1879-4.01550.22761240.16292540266496
4.0155-34.96030.22061620.17112554271696

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