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- PDB-3v8l: Crystal structure of Staphylococcus aureus biotin protein ligase ... -

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Basic information

Entry
Database: PDB / ID: 3v8l
TitleCrystal structure of Staphylococcus aureus biotin protein ligase in complex with biotinyl-5'-AMP
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: 2.6 Å
AuthorsYap, 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 1.1Mar 27, 2013Group: Experimental preparation
Revision 1.2Jul 17, 2013Group: Database references
Revision 1.3Mar 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 ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5882
Polymers38,0151
Non-polymers5741
Water5,495305
1
A: Biotin ligase
hetero molecules

A: Biotin ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1774
Polymers76,0302
Non-polymers1,1472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4260 Å2
ΔGint-21 kcal/mol
Surface area28950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.665, 93.665, 131.947
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-856-

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-BT5 / BIOTINYL-5-AMP


Type: RNA linking / Mass: 573.517 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28N7O9PS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 3.81 Å3/Da / Density % sol: 67.68 %
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: 1.518 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.518 Å / Relative weight: 1
ReflectionResolution: 2.6→39.55 Å

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→29.59 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 10.267 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23478 1359 5.1 %RANDOM
Rwork0.17417 ---
obs0.17716 25288 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2611 0 38 305 2954
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222706
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8261.963655
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9875321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.80424.929140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22215487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5731515
X-RAY DIFFRACTIONr_chiral_restr0.1180.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022045
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.21067
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21811
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2211
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.75821649
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.73232574
X-RAY DIFFRACTIONr_scbond_it2.14421215
X-RAY DIFFRACTIONr_scangle_it3.25931081
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.659 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 117 -
Rwork0.261 1823 -
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)
15.9235-2.4146-2.18986.27560.3455.079-0.0622-0.33410.2946-0.00960.1056-0.3083-0.0016-0.0834-0.0434-0.26510.1230.0427-0.11560.0201-0.174825.092424.662546.3379
21.847-0.1631-0.36642.9553-0.10072.42070.04760.07860.2627-0.05040.2290.173-0.3418-0.2521-0.2766-0.23480.02820.0529-0.12680.0708-0.132540.791217.455821.7204
37.24310.5497-3.0843.8381-0.74657.3953-0.08010.487-0.1768-0.34930.2642-0.141-0.47620.0287-0.1841-0.0252-0.0940.0663-0.20480.0797-0.341250.428918.00040.6372
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 64
2X-RAY DIFFRACTION2A65 - 263
3X-RAY DIFFRACTION3A264 - 321

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