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Yorodumi- PDB-7dbs: Crystal Structure Of Biotin Protein Ligase From Leishmania Major ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dbs | ||||||
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Title | Crystal Structure Of Biotin Protein Ligase From Leishmania Major in complex with Biotin | ||||||
Components | Biotin/lipoate protein ligase-like protein | ||||||
Keywords | LIGASE / Biotin protein ligase / Enzyme | ||||||
Function / homology | Function and homology information biotin-[biotin carboxyl-carrier protein] ligase / biotin--[biotin carboxyl-carrier protein] ligase activity / protein modification process / cytoplasm Similarity search - Function | ||||||
Biological species | Leishmania major (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | ||||||
Authors | Rajak, M. / Sundd, M. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 Title: Leishmania major biotin protein ligase forms a unique cross-handshake dimer. Authors: Rajak, M.K. / Bhatnagar, S. / Pandey, S. / Kumar, S. / Verma, S. / Patel, A.K. / Sundd, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dbs.cif.gz | 132.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dbs.ent.gz | 84.8 KB | Display | PDB format |
PDBx/mmJSON format | 7dbs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dbs_validation.pdf.gz | 713.9 KB | Display | wwPDB validaton report |
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Full document | 7dbs_full_validation.pdf.gz | 715.5 KB | Display | |
Data in XML | 7dbs_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 7dbs_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/7dbs ftp://data.pdbj.org/pub/pdb/validation_reports/db/7dbs | HTTPS FTP |
-Related structure data
Related structure data | 6jhuS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30560.057 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_31_1070 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q4Q6F6, biotin-[biotin carboxyl-carrier protein] ligase |
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#2: Chemical | ChemComp-BTN / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.9 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 19.5% PEG 3350, 200 mM Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 277.15 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979507 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979507 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→52.84 Å / Num. obs: 11509 / % possible obs: 98.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 64.68 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.027 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.332→2.372 Å / Rmerge(I) obs: 0.631 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 567 / CC1/2: 0.949 / Rpim(I) all: 0.258 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JHU Resolution: 2.33→52.84 Å / SU ML: 0.3804 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 39.9543 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.59 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.33→52.84 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 36.135690271 Å / Origin y: 0.685091776768 Å / Origin z: 38.7954802389 Å
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Refinement TLS group | Selection details: all |