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Yorodumi- PDB-3fmf: Crystal structure of Mycobacterium tuberculosis dethiobiotin synt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fmf | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase complexed with 7,8 diaminopelargonic acid carbamate | ||||||
Components | Dethiobiotin synthetase | ||||||
Keywords | LIGASE / biotin biosynthesis / Rv1570 / dethiobiotin synthetase / bioD / ATP-binding / Magnesium / Nucleotide-binding | ||||||
Function / homology | Function and homology information dethiobiotin synthase / dethiobiotin synthase activity / biotin biosynthetic process / magnesium ion binding / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Dey, S. / Sacchettini, J.C. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Structural characterization of the Mycobacterium tuberculosis biotin biosynthesis enzymes 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase . Authors: Dey, S. / Lane, J.M. / Lee, R.E. / Rubin, E.J. / Sacchettini, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fmf.cif.gz | 176.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fmf.ent.gz | 139.5 KB | Display | PDB format |
PDBx/mmJSON format | 3fmf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fmf_validation.pdf.gz | 488.2 KB | Display | wwPDB validaton report |
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Full document | 3fmf_full_validation.pdf.gz | 503.4 KB | Display | |
Data in XML | 3fmf_validation.xml.gz | 36.9 KB | Display | |
Data in CIF | 3fmf_validation.cif.gz | 51.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/3fmf ftp://data.pdbj.org/pub/pdb/validation_reports/fm/3fmf | HTTPS FTP |
-Related structure data
Related structure data | 3bv0C 3dodC 3drdC 3du4C 3fgnSC 3fmiC 3fpaC 3lv2C 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25331.891 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: bioD, MT1621, MTCY336.33c, Rv1570 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O06620, UniProt: P9WPQ5*PLUS, dethiobiotin synthase #2: Chemical | ChemComp-DSD / #3: 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: 42.64 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 50363 / % possible obs: 91.2 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 29.5 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 8.5 / % possible all: 80.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3FGN Resolution: 2.05→29.07 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.51 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.141 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→29.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.107 Å / Total num. of bins used: 20
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