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- PDB-3rkx: Structural characterisation of staphylococcus aureus biotin prote... -

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Basic information

Entry
Database: PDB / ID: 3rkx
TitleStructural characterisation of staphylococcus aureus biotin protein ligase
ComponentsBiotin-[acetyl-CoA-carboxylase] ligase
KeywordsLIGASE / biotin protein ligase / 3 domains / enzyme DNA binding / biotin carrier coupling domains
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: 2.1 Å
AuthorsWilce, M.C.J.
CitationJournal: TO BE PUBLISHED
Title: Structural characterisation of staphylococcus aureus biotin protein ligase
Authors: Pendini, N.R. / Yap, M.Y. / Polyak, S.W. / Cowieson, N. / Traore, D.A.K. / Booker, G.W. / Wallace, J.C. / Abell, A. / Wilce, J.A. / Wilce, M.C.J.
History
DepositionApr 18, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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-[acetyl-CoA-carboxylase] ligase


Theoretical massNumber of molelcules
Total (without water)37,1871
Polymers37,1871
Non-polymers00
Water3,819212
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-[acetyl-CoA-carboxylase] ligase


Mass: 37186.910 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Peg 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95364 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95364 Å / Relative weight: 1
ReflectionResolution: 2.1→35 Å / Num. obs: 18537 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RIR

3rir


Resolution: 2.1→34.956 Å / SU ML: 0.37 / σ(F): 1.38 / Phase error: 26.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2655 938 5.06 %
Rwork0.1928 --
obs0.1965 17599 96.01 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.802 Å2 / ksol: 0.386 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.2072 Å2-0 Å21.357 Å2
2---0.8081 Å20 Å2
3----0.399 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2484 0 0 212 2696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072528
X-RAY DIFFRACTIONf_angle_d1.0623410
X-RAY DIFFRACTIONf_dihedral_angle_d16.723934
X-RAY DIFFRACTIONf_chiral_restr0.075377
X-RAY DIFFRACTIONf_plane_restr0.003441
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1001-2.21080.3611410.2564246996
2.2108-2.34920.30261220.2511249595
2.3492-2.53060.29241320.2183247396
2.5306-2.78510.29151330.2042252796
2.7851-3.18790.27721240.1844254097
3.1879-4.01550.24081240.1625254196
4.0155-34.96040.23071620.1783255496
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)
10.22840.26580.16350.33840.23120.15710.1376-0.00570.00040.1817-0.055-0.20830.3152-0.1741-0.07420.2223-0.0401-0.09110.2674-0.070.173814.73517.390335.699
20.5268-0.02970.18320.54950.24620.9720.1427-0.0658-0.01170.0312-0.052-0.0195-0.05050.0571-0.0780.061-0.01650.01320.0689-0.01660.0638-4.1296-0.983713.5277
30.2932-0.2118-0.01921.0037-0.20280.26330.1014-0.096-0.0766-0.2490.0330.41320.1354-0.1126-0.09060.1471-0.0076-0.04660.08270.00030.1768-22.9604-4.5851-0.7441
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1RESSEQ 3:61
2X-RAY DIFFRACTION2RESSEQ 67:261
3X-RAY DIFFRACTION3RESSEQ 267:322

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