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Yorodumi- PDB-2ejf: Crystal Structure Of The Biotin Protein Ligase (Mutations R48A an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ejf | ||||||
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Title | Crystal Structure Of The Biotin Protein Ligase (Mutations R48A and K111A) and Biotin Carboxyl Carrier Protein Complex From Pyrococcus Horikoshii OT3 | ||||||
Components |
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Keywords | LIGASE / Biotinylation / 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-[acetyl-CoA-carboxylase] ligase activity / protein modification process / ATP binding Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Bagautdinov, B. / Matsuura, Y. / Bagautdinova, S. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Protein biotinylation visualized by a complex structure of biotin protein ligase with a substrate Authors: Bagautdinov, B. / Matsuura, Y. / Bagautdinova, S. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ejf.cif.gz | 140.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ejf.ent.gz | 107.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ejf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/2ejf ftp://data.pdbj.org/pub/pdb/validation_reports/ej/2ejf | HTTPS FTP |
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-Related structure data
Related structure data | 1x01C 2d5dSC 2dxuC 2dzcC 2e41C 2e64SC 2ejgC 2evbC 2zgwC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-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
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 25959.305 Da / Num. of mol.: 2 / Mutation: R48A/K111A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: bpl / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): (DE3)RIL / References: UniProt: O57883 #2: Protein | Mass: 7985.457 Da / Num. of mol.: 2 / Fragment: residues 77-149 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: bccp / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): (DE3)RIL / References: UniProt: O59021 |
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-Non-polymers , 4 types, 415 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: 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: 2.44 Å3/Da / Density % sol: 49.63 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 4.96 Details: 10.5w/v(%) PEG 20000, 0.1M Acet, NaOH, pH 4.96, microbatch, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 12, 2006 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→37.62 Å / Num. obs: 42136 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.071 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3935 / Rsym value: 0.298 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2E64 AND 2D5D Resolution: 2→37.62 Å / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 28.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→37.62 Å
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Refine LS restraints |
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