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- PDB-2ejf: Crystal Structure Of The Biotin Protein Ligase (Mutations R48A an... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ejf | ||||||
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Title | Crystal Structure Of The Biotin Protein Ligase (Mutations R48A and K111A) and Biotin Carboxyl Carrier Protein Complex From Pyrococcus Horikoshii OT3 | ||||||
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![]() | LIGASE / Biotinylation / 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. / Matsuura, Y. / Bagautdinova, S. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.7 KB | Display | ![]() |
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PDB format | ![]() | 107.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1x01C ![]() 2d5dSC ![]() 2dxuC ![]() 2dzcC ![]() 2e41C ![]() 2e64SC ![]() 2ejgC ![]() 2evbC ![]() 2zgwC C: citing same article ( S: Starting model for refinement |
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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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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 25959.305 Da / Num. of mol.: 2 / Mutation: R48A/K111A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 7985.457 Da / Num. of mol.: 2 / Fragment: residues 77-149 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 415 molecules ![](data/chem/img/BTN.gif)
![](data/chem/img/ADN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ADN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.63 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 4.96 Details: 10.5w/v(%) PEG 20000, 0.1M Acet, NaOH, pH 4.96, microbatch, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 12, 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: 2→37.62 Å / Num. obs: 42136 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.071 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3935 / Rsym value: 0.298 / % possible all: 90 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 2E64 AND 2D5D Resolution: 2→37.62 Å / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 28.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→37.62 Å
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Refine LS restraints |
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