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- PDB-4ha8: Structure of Staphylococcus aureus biotin protein ligase in compl... -

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Basic information

Entry
Database: PDB / ID: 4ha8
TitleStructure of Staphylococcus aureus biotin protein ligase in complex with biotin acetylene
ComponentsBiotin-[acetyl-CoA-carboxylase] ligase
KeywordsLIGASE / DNA-binding domain
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: 2.65 Å
AuthorsYap, M. / Wilce, M. / Polyak, S / Soares da Costa, T. / Tieu, W.
CitationJournal: To be Published
Title: Structure of Staphylococcus aureus biotin protein ligase in complex with biotin acetylene
Authors: Yap, M. / Wilce, M. / Polyak, S / Soares da Costa, T. / Tieu, W.
History
DepositionSep 25, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,1092
Polymers37,8851
Non-polymers2241
Water2,630146
1
A: Biotin-[acetyl-CoA-carboxylase] ligase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)76,2184
Polymers75,7692
Non-polymers4492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area3240 Å2
ΔGint-13 kcal/mol
Surface area28590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.020, 93.020, 129.940
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-574-

HOH

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Components

#1: Protein Biotin-[acetyl-CoA-carboxylase] ligase


Mass: 37884.590 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-BC4 / (3aS,4S,6aR)-4-(hex-5-yn-1-yl)tetrahydro-1H-thieno[3,4-d]imidazol-2(3H)-one / biotin acetylene


Mass: 224.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N2OS
#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: 3.71 Å3/Da / Density % sol: 66.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 8000, 0.1M Tris pH 7.5, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.65 Å / Num. all: 17103 / Num. obs: 16247

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Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.5.0102refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→19.81 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.91 / SU B: 8.576 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23594 856 5 %RANDOM
Rwork0.19696 ---
obs0.19889 16247 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: 45.958 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: 2.65→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2613 0 15 146 2774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222679
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8651.9463612
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0365321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.18624.929140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.65715487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3891515
X-RAY DIFFRACTIONr_chiral_restr0.120.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022028
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_it0.9951.51596
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.02522572
X-RAY DIFFRACTIONr_scbond_it3.15231083
X-RAY DIFFRACTIONr_scangle_it5.3274.51040
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.649→2.717 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 60 -
Rwork0.296 1124 -
obs--100 %

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