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- PDB-2dth: The Crystal Structure of the Orthorhombic Form of Biotin Protein ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2dth | ||||||
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Title | The Crystal Structure of the Orthorhombic Form of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotin and ADP | ||||||
![]() | 235aa long hypothetical biotin--[acetyl-CoA-carboxylase] 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--[biotin carboxyl-carrier protein] 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 | ![]() | 119.3 KB | Display | ![]() |
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PDB format | ![]() | 91.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 28 KB | Display | |
Data in CIF | ![]() | 41.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2dkgC ![]() 2dtoC ![]() 2dxtC ![]() 2dz9C ![]() 2e1hC ![]() 2e65C ![]() 2fykSC 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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1 |
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Unit cell |
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Details | The biological unit is a dimer identical to the asymmetric unit |
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Components
#1: Protein | Mass: 26103.523 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: 2.54 Å3/Da / Density % sol: 51.56 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 5.2 Details: PEG20K, Acetate, NaOH, 2.5mM ADP, 2.5mM Biotin, 1mM MnCl2, pH 5.2, microbatch, 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: Jun 23, 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: 1.95→50 Å / Num. all: 39486 / Num. obs: 38943 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 26.22 Å2 / Rmerge(I) obs: 0.124 / Rsym value: 0.097 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3873 / Rsym value: 0.395 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2FYK Resolution: 1.95→36.24 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: 35.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→36.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.02 Å / Rfactor Rfree error: 0.021
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