[English] 日本語
Yorodumi- PDB-1x01: Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horiko... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x01 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horikoshii Ot3 in complex with ATP | ||||||
Components | biotin--[acetyl-CoA-carboxylase] ligase | ||||||
Keywords | LIGASE / Biotin Protein Ligase / Dimer / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses | ||||||
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 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1x01.cif.gz | 113.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1x01.ent.gz | 86.7 KB | Display | PDB format |
PDBx/mmJSON format | 1x01.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x0/1x01 ftp://data.pdbj.org/pub/pdb/validation_reports/x0/1x01 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2d5dC 2dxuC 2dzcC 2e41C 2e64C 2ejfC 2ejgC 2evbC 2zgwC 1wq7S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 | ChemComp-PO4 / | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.5 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.2 Details: PEG20K, Acetate, NaOH, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 12, 2004 / 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→40 Å / Num. all: 29087 / Num. obs: 29015 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2837 / % possible all: 94.9 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1wq7 Resolution: 2→32.39 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.5 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→32.39 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2
|