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- PDB-4dq2: Structure of staphylococcus aureus biotin protein ligase in compl... -

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Basic information

Entry
Database: PDB / ID: 4dq2
TitleStructure of staphylococcus aureus biotin protein ligase in complex with biotinol-5'-amp
ComponentsBiotin-[acetyl-CoA-carboxylase] ligase
KeywordsLIGASE / DNA binding domain / metabolism / biotin / ligate
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: 2.5 Å
AuthorsWilce, M. / Yap, M. / Pendini, N. / Soares de Costa, T. / Polyak, S. / Tieu, W. / Booker, G. / Wallace, J.
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
DepositionFeb 14, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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-[acetyl-CoA-carboxylase] ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4432
Polymers37,8841
Non-polymers5601
Water1,892105
1
A: Biotin-[acetyl-CoA-carboxylase] ligase
hetero molecules

A: Biotin-[acetyl-CoA-carboxylase] ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8864
Polymers75,7672
Non-polymers1,1192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4400 Å2
ΔGint-21 kcal/mol
Surface area28580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.598, 94.598, 130.626
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 Biotin-[acetyl-CoA-carboxylase] ligase


Mass: 37883.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: ECT-R 2 / Gene: ECTR2_1310 / Production host: Escherichia coli (E. coli)
References: UniProt: E5R5T0, biotin-[biotin carboxyl-carrier protein] ligase
#2: Chemical ChemComp-BTX / ((2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHYL 5-((3AS,4S,6AR)-2-OXO-HEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL)PENTYL HYDROGEN PHOSPHATE / BIOTINOL-5-AMP


Mass: 559.533 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30N7O8PS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 3.86 Å3/Da / Density % sol: 68.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 8000, 0.1M Tris-HCl pH 7.5, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1.5418 Å
DetectorDate: Sep 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→39.55 Å / Num. obs: 20793

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Processing

SoftwareName: REFMAC / Version: 5.5.0102 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→39.55 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.919 / SU B: 13.312 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23932 1065 5.1 %RANDOM
Rwork0.19092 ---
obs0.19341 19687 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: 33.315 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å2-0 Å2-0 Å2
2--0.68 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2610 0 37 105 2752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222704
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2141.9593651
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1885321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.24724.929140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.23915487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1061515
X-RAY DIFFRACTIONr_chiral_restr0.1360.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022037
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_it1.0571.51596
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.09722572
X-RAY DIFFRACTIONr_scbond_it3.55331108
X-RAY DIFFRACTIONr_scangle_it5.6244.51079
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 80 -
Rwork0.315 1431 -
obs--100 %
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)
12.5985-1.9245-1.81134.46871.27792.05270.1415-0.12550.1563-0.20260.0216-0.0875-0.0658-0.0257-0.16320.13650.06390.0330.10820.04710.09726.19124.28245.538
20.64990.1739-0.34881.1144-0.02231.38980.07220.10230.04160.04740.13770.0954-0.2123-0.1324-0.20990.12040.0060.05150.14220.04720.105341.95317.51919.418
32.95270.0301-1.56491.14860.54166.2843-0.0040.2716-0.0652-0.12220.1168-0.0058-0.05510.1363-0.11280.1541-0.07140.04980.19110.00980.038253.56216.406-0.415
45.14862.23227.61792.28175.460814.9539-0.44170.2560.3605-0.03620.3006-0.1091-0.40530.6210.14110.2056-0.02370.0840.1001-0.02950.319851.74319.69121.303
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 68
2X-RAY DIFFRACTION2A69 - 288
3X-RAY DIFFRACTION3A289 - 323
4X-RAY DIFFRACTION4A500

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