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- PDB-4wf2: Structure of E. coli BirA G142A bound to biotinol-5'-AMP -

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Basic information

Entry
Database: PDB / ID: 4wf2
TitleStructure of E. coli BirA G142A bound to biotinol-5'-AMP
ComponentsBifunctional ligase/repressor BirA
KeywordsLIGASE / biotin protein ligase / biotin repressor / G142A mutant / complex with biotinol-5'-AMP
Function / homology
Function and homology information


biotin metabolic process / biotin-[biotin carboxyl-carrier protein] ligase / biotin-[acetyl-CoA-carboxylase] ligase activity / biotin biosynthetic process / biotin binding / transcription repressor complex / protein modification process / nucleic acid binding / transcription cis-regulatory region binding / regulation of DNA-templated transcription ...biotin metabolic process / biotin-[biotin carboxyl-carrier protein] ligase / biotin-[acetyl-CoA-carboxylase] ligase activity / biotin biosynthetic process / biotin binding / transcription repressor complex / protein modification process / nucleic acid binding / transcription cis-regulatory region binding / regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / ATP binding / cytoplasm
Similarity search - Function
Biotin operon repressor, helix-turn-helix domain / Bifunctional ligase/repressor BirA / Helix-turn-helix, type 11 / HTH domain / 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 ...Biotin operon repressor, helix-turn-helix domain / Bifunctional ligase/repressor BirA / Helix-turn-helix, type 11 / HTH domain / 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 / Transcriptional repressor, C-terminal / 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) / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / SH3 type barrels. / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Roll / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-BTX / Bifunctional ligase/repressor BirA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.31 Å
AuthorsEginton, C. / Beckett, D. / Wade, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-0953430 United States
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Allosteric Coupling via Distant Disorder-to-Order Transitions.
Authors: Eginton, C. / Cressman, W.J. / Bachas, S. / Wade, H. / Beckett, D.
History
DepositionSep 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Mar 25, 2015Group: Database references
Revision 1.3Apr 8, 2015Group: Database references
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.5Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional ligase/repressor BirA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7542
Polymers36,1951
Non-polymers5601
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.239, 46.239, 157.107
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Bifunctional ligase/repressor BirA / Biotin operon repressor / Biotin--[acetyl-CoA-carboxylase] ligase / Biotin--protein ligase / Biotin- ...Biotin operon repressor / Biotin--[acetyl-CoA-carboxylase] ligase / Biotin--protein ligase / Biotin-[acetyl-CoA carboxylase] synthetase


Mass: 36194.812 Da / Num. of mol.: 1 / Mutation: G142A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: birA, bioR, dhbB, b3973, JW3941 / Plasmid: pBtac2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: P06709, biotin-[biotin carboxyl-carrier protein] ligase
#2: Chemical ChemComp-BTX / ((2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHYL 5-((3AS,4S,6AR)-2-OXO-HEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL)PENTYL HYDROGEN PHOSPHATE / BIOTINOL-5-AMP


Mass: 559.533 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30N7O8PS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M TrisHCl, pH 8.0 and 12.5% (w/v) PEG 8K (Hampton) at 20 deg C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.31→50 Å / Num. obs: 14338 / % possible obs: 99.42 % / Redundancy: 3.2 % / Net I/σ(I): 11.68

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 2.31→39.85 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 20.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2183 723 5.04 %
Rwork0.1721 --
obs0.1744 14334 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.31→39.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2352 0 37 135 2524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042445
X-RAY DIFFRACTIONf_angle_d0.8023310
X-RAY DIFFRACTIONf_dihedral_angle_d14.229904
X-RAY DIFFRACTIONf_chiral_restr0.029373
X-RAY DIFFRACTIONf_plane_restr0.003419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.48720.25661490.20732613X-RAY DIFFRACTION97
2.4872-2.73740.25411490.19852741X-RAY DIFFRACTION100
2.7374-3.13310.23761520.19632745X-RAY DIFFRACTION100
3.1331-3.9460.22511490.16762723X-RAY DIFFRACTION100
3.946-30.18810.17991240.14912789X-RAY DIFFRACTION100

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