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Yorodumi- PDB-4op0: Crystal structure of biotin protein ligase (RV3279C) of Mycobacte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4op0 | ||||||
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Title | Crystal structure of biotin protein ligase (RV3279C) of Mycobacterium tuberculosis, complexed with biotinyl-5'-AMP | ||||||
Components | BirA bifunctional protein | ||||||
Keywords | LIGASE / BIRA | ||||||
Function / homology | Function and homology information biotin-protein ligase activity / biotin-[biotin carboxyl-carrier protein] ligase / biotin-[acetyl-CoA-carboxylase] ligase activity / biotin binding / small molecule binding / post-translational protein modification / protein modification process / positive regulation of cell population proliferation / protein homodimerization activity / protein-containing complex ...biotin-protein ligase activity / biotin-[biotin carboxyl-carrier protein] ligase / biotin-[acetyl-CoA-carboxylase] ligase activity / biotin binding / small molecule binding / post-translational protein modification / protein modification process / positive regulation of cell population proliferation / protein homodimerization activity / protein-containing complex / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Ma, Q. / Wilmanns, M. / Akhter, Y. | ||||||
Citation | Journal: Protein Sci. / Year: 2014 Title: Active site conformational changes upon reaction intermediate biotinyl-5'-AMP binding in biotin protein ligase from Mycobacterium tuberculosis. Authors: Ma, Q. / Akhter, Y. / Wilmanns, M. / Ehebauer, M.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4op0.cif.gz | 210.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4op0.ent.gz | 168.5 KB | Display | PDB format |
PDBx/mmJSON format | 4op0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/4op0 ftp://data.pdbj.org/pub/pdb/validation_reports/op/4op0 | HTTPS FTP |
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-Related structure data
Related structure data | 2cghSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28251.129 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: birA, MT3379, Rv3279c / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS References: UniProt: P96884, UniProt: I6YFP0*PLUS, biotin-[biotin carboxyl-carrier protein] ligase #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 0.1 M Tris-HCl, pH 7.8, 0.2 M lithium sulfate, 25% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9762 / Wavelength: 0.9762 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 26, 2006 Details: mirrors: 1: Rh-coated, zerodur, vertical focusing possible, 2: Rh-coated, zerodur, vertically focusing |
Radiation | Monochromator: fixed exit double crystal Si(111), horizontally focusing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→31.36 Å / Num. obs: 51119 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12 % / Biso Wilson estimate: 24.2 Å2 / Rsym value: 0.098 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 3.25 / Num. unique all: 7904 / Rsym value: 0.526 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CGH Resolution: 1.7→31.36 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.687 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.938 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→31.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.74 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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