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- PDB-2eay: Crystal Structure Of Biotin Protein Ligase From Aquifex Aeolicus -

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Basic information

Entry
Database: PDB / ID: 2eay
TitleCrystal Structure Of Biotin Protein Ligase From Aquifex Aeolicus
ComponentsBiotin [acetyl-CoA-carboxylase] ligase
KeywordsLIGASE / Biotin Biosynthesis / Dimer / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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: 1.95 Å
AuthorsBagautdinov, B. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure Of Biotin Protein Ligase From Aquifex Aeolicus
Authors: Bagautdinov, B. / Kunishima, N.
History
DepositionFeb 4, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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


Theoretical massNumber of molelcules
Total (without water)53,5822
Polymers53,5822
Non-polymers00
Water5,837324
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.076, 60.589, 73.106
Angle α, β, γ (deg.)90.00, 91.99, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a dimer and identical to the asymmetric unit

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Components

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


Mass: 26790.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: birA / Plasmid: pET 11a / Production host: Escherichia coli (E. coli) / Strain (production host): (DE3)RIL
References: UniProt: O66837, biotin-[biotin carboxyl-carrier protein] ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.27 Å3/Da / Density % sol: 45.93 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7.4
Details: 27.5w/v(%) PEG 4K, 0.1M Hepes-NaOH, pH 7.4, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 2, 2006 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→36.53 Å / Num. all: 35262 / Num. obs: 33213 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 37.9 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.044 / Net I/σ(I): 14.7
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3367 / Rsym value: 0.272 / % possible all: 96.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wqw

1wqw


Resolution: 1.95→36.53 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1649 -RANDOM
Rwork0.214 ---
obs0.214 33213 94.2 %-
all-35262 --
Displacement parametersBiso mean: 39.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.57 Å20 Å210.29 Å2
2---0.93 Å20 Å2
3----1.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.95→36.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3555 0 0 324 3879
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.91
LS refinement shellResolution: 1.95→2.02 Å / Rfactor Rfree error: 0.025
RfactorNum. reflection% reflection
Rfree0.302 143 -
Rwork0.294 --
obs-2992 84.8 %

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