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- PDB-3efr: Biotin protein ligase R40G mutant from Aquifex aeolicus in comple... -

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Basic information

Entry
Database: PDB / ID: 3efr
TitleBiotin protein ligase R40G mutant from Aquifex aeolicus in complex with biotin
ComponentsBiotin [acetyl-CoA-carboxylase] ligase
KeywordsLIGASE / Protein biotin complex
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--[biotin carboxyl-carrier protein] ligase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsTron, C.M. / McNae, I.W. / Walkinshaw, M.D. / Baxter, R.L. / 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
DepositionSep 10, 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 10, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)54,1758
Polymers53,3022
Non-polymers8736
Water1,31573
1
A: Biotin [acetyl-CoA-carboxylase] ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1835
Polymers26,6511
Non-polymers5324
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)26,9913
Polymers26,6511
Non-polymers3402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.251, 79.928, 140.173
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 26650.953 Da / Num. of mol.: 2 / Mutation: R40G
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-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.17 Å3/Da / Density % sol: 43.26 %
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: 0.978 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 6, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.55→28.841 Å / Num. obs: 13851 / % possible obs: 88.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 45.53 Å2 / Rsym value: 0.097 / Net I/σ(I): 12.6
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 1869 / Rsym value: 0.639 / % possible all: 83.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WPY

1wpy


Resolution: 2.55→28.841 Å / Occupancy max: 1 / Occupancy min: 0.14 / SU ML: 0.49 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.289 687 4.97 %RANDOM
Rwork0.235 13133 --
obs0.237 13820 87.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.961 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 122.64 Å2 / Biso mean: 47.349 Å2 / Biso min: 17.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.175 Å20 Å20 Å2
2--0.156 Å20 Å2
3----0.331 Å2
Refine analyzeLuzzati sigma a obs: 0.378 Å
Refinement stepCycle: LAST / Resolution: 2.55→28.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3749 0 52 73 3874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023858
X-RAY DIFFRACTIONf_angle_d0.715169
X-RAY DIFFRACTIONf_chiral_restr0.044573
X-RAY DIFFRACTIONf_plane_restr0.003639
X-RAY DIFFRACTIONf_dihedral_angle_d15.6441499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5501-2.74680.40571220.30852444X-RAY DIFFRACTION83
2.7468-3.0230.35241360.28422442X-RAY DIFFRACTION84
3.023-3.45980.27611280.24772489X-RAY DIFFRACTION83
3.4598-4.35650.2561480.20412680X-RAY DIFFRACTION90
4.3565-28.84240.27291530.2173078X-RAY DIFFRACTION97

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