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Yorodumi- PDB-2d5d: Structure of Biotin Carboxyl Carrier Protein (74Val start) from P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d5d | ||||||
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Title | Structure of Biotin Carboxyl Carrier Protein (74Val start) from Pyrococcus horikoshi OT3 Ligand Free Form II | ||||||
Components | methylmalonyl-CoA decarboxylase gamma chain | ||||||
Keywords | LIPID BINDING PROTEIN / TRANSFERASE / Biotin / BCCP / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information Biotin-binding site / Biotin-requiring enzymes attachment site. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Bagautdinov, B. / 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 | 2d5d.cif.gz | 41.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d5d.ent.gz | 29.3 KB | Display | PDB format |
PDBx/mmJSON format | 2d5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2d5d_validation.pdf.gz | 436.5 KB | Display | wwPDB validaton report |
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Full document | 2d5d_full_validation.pdf.gz | 441.9 KB | Display | |
Data in XML | 2d5d_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 2d5d_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/2d5d ftp://data.pdbj.org/pub/pdb/validation_reports/d5/2d5d | HTTPS FTP |
-Related structure data
Related structure data | 1x01C 2dxuC 2dzcC 2e41C 2e64C 2ejfC 2ejgC 2evbSC 2zgwC S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 7985.457 Da / Num. of mol.: 2 / Fragment: residues 73-146 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: bccp / Plasmid: PET 11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: O59021, methylmalonyl-CoA carboxytransferase #2: 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: 2.18 Å3/Da / Density % sol: 43.65 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 5.06 Details: PEG 20K 10.5w/w(%), Acetate, NaOH, pH 5.06, 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: Oct 2, 2005 / 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: 1.55→26.77 Å / Num. all: 21006 / Num. obs: 20701 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 23.73 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 27.7 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 3.12 / Num. unique all: 2024 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2EVB Resolution: 1.55→26.77 Å / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 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: 1.55→26.77 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2
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