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- PDB-3l2z: Crystal structure of hydrated Biotin Protein Ligase from M. tuber... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3l2z | ||||||
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Title | Crystal structure of hydrated Biotin Protein Ligase from M. tuberculosis | ||||||
![]() | BirA bifunctional protein | ||||||
![]() | LIGASE / BirA / hydrated structure / disordered ligand binding loops | ||||||
Function / homology | ![]() : / biotin-[biotin carboxyl-carrier protein] ligase / biotin--[biotin carboxyl-carrier protein] ligase activity / small molecule binding / post-translational protein modification / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gupta, V. / Gupta, R.K. / Khare, G. / Salunke, D.M. / Tyagi, A.K. | ||||||
![]() | ![]() Title: Structural ordering of disordered ligand-binding loops of biotin protein ligase into active conformations as a consequence of dehydration. Authors: Gupta, V. / Gupta, R.K. / Khare, G. / Salunke, D.M. / Surolia, A. / Tyagi, A.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.8 KB | Display | ![]() |
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PDB format | ![]() | 76.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.3 KB | Display | ![]() |
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Full document | ![]() | 462.2 KB | Display | |
Data in XML | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 27.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3l1aC ![]() 2cghS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28153.027 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P96884, biotin-[biotin carboxyl-carrier protein] ligase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 12-16% PEG4000, PEG8000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 21, 2007 / Details: bending magnet |
Radiation | Monochromator: Si 111, horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8088 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→15 Å / Num. obs: 15831 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 2.2 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2CGH Resolution: 2.8→14.126 Å / SU ML: 0.66 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.61 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.366 Å2 / ksol: 0.309 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.8→14.126 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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