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- PDB-3v7r: Crystal structure of Staphylococcus aureus biotin protein ligase ... -

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Basic information

Entry
Database: PDB / ID: 3v7r
TitleCrystal structure of Staphylococcus aureus biotin protein ligase in complex with inhibitor
ComponentsBiotin ligase
KeywordsLIGASE/LIGASE INHIBITOR / biotin / metabolism / biotin carboxyl carrier protein / LIGASE-LIGASE INHIBITOR complex
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 / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsYap, M.Y. / Pendini, N.R.
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 21, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Biotin ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4852
Polymers38,0151
Non-polymers4711
Water2,630146
1
A: Biotin ligase
hetero molecules

A: Biotin ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9714
Polymers76,0302
Non-polymers9412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area2150 Å2
ΔGint-7 kcal/mol
Surface area28510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.600, 94.600, 130.680
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-674-

HOH

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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: Chemical ChemComp-32G / (3aS,4S,6aR)-4-(5-{1-[4-(6-amino-9H-purin-9-yl)butyl]-1H-1,2,3-triazol-4-yl}pentyl)tetrahydro-1H-thieno[3,4-d]imidazol-2(3H)-one


Mass: 470.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N10OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 3.85 Å3/Da / Density % sol: 68.01 %
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: 1.54 Å
DetectorDate: Sep 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.61→19.85 Å / Num. obs: 18442

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Processing

SoftwareName: REFMAC / Version: 5.5.0102 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RKW

3rkw


Resolution: 2.61→19.85 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.899 / SU B: 8.838 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.353 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 923 5 %RANDOM
Rwork0.20034 ---
obs0.20286 17519 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.426 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2---0.4 Å2-0 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 2.61→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2610 0 33 146 2789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222700
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9771.9553642
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2585321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.14124.929140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.63415487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3751515
X-RAY DIFFRACTIONr_chiral_restr0.1360.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022046
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1071.51596
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.23722572
X-RAY DIFFRACTIONr_scbond_it3.22431104
X-RAY DIFFRACTIONr_scangle_it5.3574.51070
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.612→2.679 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 63 -
Rwork0.27 1186 -
obs--100 %

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