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Yorodumi- PDB-3tao: Structure of Mycobacterium tuberculosis triosephosphate isomerase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tao | ||||||
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Title | Structure of Mycobacterium tuberculosis triosephosphate isomerase bound to phosphoglycolohydroxamate | ||||||
Components | Triosephosphate isomerase | ||||||
Keywords | ISOMERASE | ||||||
Function / homology | Function and homology information glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / extracellular region / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å | ||||||
Authors | Connor, S.E. / Capodagli, G.C. / Deaton, M.K. / Pegan, S.D. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2011 Title: Structural and functional characterization of Mycobacterium tuberculosis triosephosphate isomerase. Authors: Connor, S.E. / Capodagli, G.C. / Deaton, M.K. / Pegan, S.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tao.cif.gz | 131.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tao.ent.gz | 102.5 KB | Display | PDB format |
PDBx/mmJSON format | 3tao.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ta/3tao ftp://data.pdbj.org/pub/pdb/validation_reports/ta/3tao | HTTPS FTP |
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-Related 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: 28262.898 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT1482, MTCY493.16c, Rv1438, tpi, tpiA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P66940, UniProt: P9WG43*PLUS, triose-phosphate isomerase #2: Chemical | #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: 2.36 Å3/Da / Density % sol: 47.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 16% PEG3350, 250 mM ammonium citrate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 20, 2010 |
Radiation | Monochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→74.65 Å / Num. all: 97577 / Num. obs: 94064 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.45→1.48 Å / % possible all: 86.2 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 38.65 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→28.882 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.1904 / WRfactor Rwork: 0.1688 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.8974 / SU B: 0.92 / SU ML: 0.037 / SU R Cruickshank DPI: 0.0644 / SU Rfree: 0.0646 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 107.91 Å2 / Biso mean: 16.6868 Å2 / Biso min: 4.36 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→28.882 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Total num. of bins used: 20
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