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- PDB-2fyk: Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horiko... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2fyk | ||||||
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Title | Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in complex with ADP and Biotin | ||||||
![]() | biotin--protein ligase | ||||||
![]() | LIGASE / Biotin Biosynthesis / Dimer / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | ![]() biotin-[acetyl-CoA-carboxylase] ligase activity / protein modification process / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bagautdinov, B. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.4 KB | Display | ![]() |
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PDB format | ![]() | 92.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 28.2 KB | Display | |
Data in CIF | ![]() | 41.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2dkgC ![]() 2dthC ![]() 2dtoC ![]() 2dxtC ![]() 2dz9C ![]() 2e1hC ![]() 2e65C ![]() 1wq7S S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly is a dimer |
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Components
#1: Protein | Mass: 26337.998 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O57883, biotin-[biotin carboxyl-carrier protein] ligase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.49 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 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: 1.6→40 Å / Num. all: 58407 / Num. obs: 57460 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.037 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 3.8 / Num. unique all: 5170 / Rsym value: 0.151 / % possible all: 88.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1WQ7 Resolution: 1.6→27.78 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: 22.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→27.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.66 Å / Rfactor Rfree error: 0.017
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