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Yorodumi- PDB-3efr: Biotin protein ligase R40G mutant from Aquifex aeolicus in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3efr | ||||||
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Title | Biotin protein ligase R40G mutant from Aquifex aeolicus in complex with biotin | ||||||
Components | Biotin [acetyl-CoA-carboxylase] ligase | ||||||
Keywords | LIGASE / Protein biotin complex | ||||||
Function / homology | Function and homology information biotin-[biotin carboxyl-carrier protein] ligase / biotin-[acetyl-CoA-carboxylase] ligase activity / protein modification process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Tron, C.M. / McNae, I.W. / Walkinshaw, M.D. / Baxter, R.L. / Campopiano, D.J. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3efr.cif.gz | 107 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3efr.ent.gz | 82.1 KB | Display | PDB format |
PDBx/mmJSON format | 3efr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/3efr ftp://data.pdbj.org/pub/pdb/validation_reports/ef/3efr | HTTPS FTP |
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-Related structure data
Related structure data | 3efsC 3fjpC 1wpyS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | 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 | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.26 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.978 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 6, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage 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 parameters | Biso max: 122.64 Å2 / Biso mean: 47.349 Å2 / Biso min: 17.79 Å2
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Refine analyze | Luzzati sigma a obs: 0.378 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→28.841 Å
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Refine LS restraints |
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LS refinement shell |
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