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- PDB-3fjp: Apo structure of Biotin protein ligase from Aquifex aeolicus -

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Basic information

Entry
Database: PDB / ID: 3fjp
TitleApo structure of Biotin protein ligase from Aquifex aeolicus
ComponentsBiotin [acetyl-CoA-carboxylase] ligase
KeywordsLIGASE / BPL / biotin protein ligase
Function / homology
Function and homology information


biotin-[biotin carboxyl-carrier protein] ligase / biotin--[biotin carboxyl-carrier protein] ligase activity / protein modification process / ATP binding / cytoplasm
Similarity search - Function
Biotin protein ligase, C-terminal / Biotin protein ligase C terminal domain / Biotin--acetyl-CoA-carboxylase ligase / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile. / Biotin/lipoate A/B protein ligase family / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain / SH3 type barrels. - #100 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) ...Biotin protein ligase, C-terminal / Biotin protein ligase C terminal domain / Biotin--acetyl-CoA-carboxylase ligase / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile. / Biotin/lipoate A/B protein ligase family / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain / SH3 type barrels. - #100 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / SH3 type barrels. / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
biotin--[biotin carboxyl-carrier protein] ligase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMcNae, I.W. / Tron, C.M. / Baxter, R.L. / Walkinshaw, M.D. / Campopiano, D.J.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural and functional studies of the biotin protein ligase from Aquifex aeolicus reveal a critical role for a conserved residue in target specificity.
Authors: Tron, C.M. / McNae, I.W. / Nutley, M. / Clarke, D.J. / Cooper, A. / Walkinshaw, M.D. / Baxter, R.L. / Campopiano, D.J.
History
DepositionDec 15, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2019Group: Data collection / Database references / Category: citation / struct_ref_seq_dif
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Biotin [acetyl-CoA-carboxylase] ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6944
Polymers53,5022
Non-polymers1922
Water1,06359
1
A: Biotin [acetyl-CoA-carboxylase] ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8472
Polymers26,7511
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Biotin [acetyl-CoA-carboxylase] ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8472
Polymers26,7511
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.533, 61.342, 73.283
Angle α, β, γ (deg.)90.00, 90.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 26751.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: PET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: O66837, biotin-[biotin carboxyl-carrier protein] ligase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.37 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, 0.2M AMMONIUM SULPHATE, 15% MPEG 5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.968 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 4, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.3→31.47 Å / Num. obs: 20759 / % possible obs: 92.4 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 49.21 Å2 / Rsym value: 0.035 / Net I/σ(I): 22.4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 5 / Num. unique all: 2066 / Rsym value: 0.308 / % possible all: 64.6

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WPY

1wpy


Resolution: 2.3→30.867 Å / SU ML: 0.42 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2793 1055 5.08 %RANDOM
Rwork0.22 ---
obs0.2229 20745 92.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.394 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso mean: 50.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.342 Å
Refinement stepCycle: LAST / Resolution: 2.3→30.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3557 0 10 59 3626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123617
X-RAY DIFFRACTIONf_angle_d1.3684846
X-RAY DIFFRACTIONf_chiral_restr0.083546
X-RAY DIFFRACTIONf_plane_restr0.004601
X-RAY DIFFRACTIONf_dihedral_angle_d19.7671395
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.4050.331920.2831632172462
2.405-2.5310.3461390.2722292243187
2.531-2.690.311510.2692587273898
2.69-2.8980.3511350.262589272498
2.898-3.1890.3191540.2542603275798
3.189-3.650.3051360.2172609274598
3.65-4.5960.2441220.1912682280499
4.596-30.870.2291260.1922710283698

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