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Yorodumi- PDB-2e65: Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horiko... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2.0E+65 | ||||||
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Title | Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horikoshii OT3, Mutation D104A | ||||||
Components | 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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.65 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 | 2e65.cif.gz | 109.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e65.ent.gz | 83.6 KB | Display | PDB format |
PDBx/mmJSON format | 2e65.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2e65_validation.pdf.gz | 434 KB | Display | wwPDB validaton report |
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Full document | 2e65_full_validation.pdf.gz | 442.3 KB | Display | |
Data in XML | 2e65_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 2e65_validation.cif.gz | 35.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/2e65 ftp://data.pdbj.org/pub/pdb/validation_reports/e6/2e65 | HTTPS FTP |
-Related structure data
Related structure data | 2dkgC 2dthC 2dtoC 2dxtSC 2dz9C 2e1hC 2fykC 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: 26059.514 Da / Num. of mol.: 2 / Mutation: D104A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: bpl / Plasmid: pET 11a / Production host: Escherichia coli (E. coli) / Strain (production host): (DE3)RIL References: UniProt: O57883, biotin-[biotin carboxyl-carrier protein] ligase #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: 2.15 Å3/Da / Density % sol: 42.78 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 5.2 Details: PEG20K, Acetate, NaOH, pH 5.2, 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: Nov 25, 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: 1.65→41.3 Å / Num. all: 52629 / Num. obs: 50943 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.058 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4713 / Rsym value: 0.258 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2DXT Resolution: 1.65→36.62 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: 26.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→36.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.71 Å / Rfactor Rfree error: 0.021
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