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Yorodumi- PDB-2dti: Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horiko... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dti | ||||||
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Title | Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotinyl-5'-AMP, Pyrophosphate and Mn(2+) | ||||||
Components | 235aa long hypothetical biotin-[acetyl-CoA-carboxylase] ligase | ||||||
Keywords | LIGASE / 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 activity / protein modification process / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.2 Å | ||||||
Authors | Bagautdinov, B. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Ligand Structures Of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 Authors: Bagautdinov, B. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dti.cif.gz | 119.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dti.ent.gz | 89.9 KB | Display | PDB format |
PDBx/mmJSON format | 2dti.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dti_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2dti_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2dti_validation.xml.gz | 28 KB | Display | |
Data in CIF | 2dti_validation.cif.gz | 40.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/2dti ftp://data.pdbj.org/pub/pdb/validation_reports/dt/2dti | HTTPS FTP |
-Related structure data
Related structure data | 2deqC 2djzC 2hniC 2dkgS 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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Unit cell |
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Details | The biological unit is a dimer and identical to the asymmetric unit |
-Components
#1: Protein | Mass: 26103.523 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: birA / Plasmid: pET 11a / Production host: Escherichia coli (E. coli) / Strain (production host): (DE3)RIL References: UniProt: O57883, biotin-[biotin carboxyl-carrier protein] ligase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.16 Å3/Da / Density % sol: 42.96 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.2 Details: PEG 20K, Acetate, NaOH, ATP, biotin, Mn(2+) , pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 25, 2005 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 22593 / Num. obs: 20276 / % possible obs: 89.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 27.81 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.054 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 7.6 / Num. unique all: 2055 / Rsym value: 0.165 / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2DKG Resolution: 2.2→35.54 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: 33.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→35.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Rfactor Rfree error: 0.034
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