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Yorodumi- PDB-3rim: Crystal structure of mycobacterium tuberculosis Transketolase (Rv... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rim | ||||||
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Title | Crystal structure of mycobacterium tuberculosis Transketolase (Rv1449c) | ||||||
Components | Transketolase | ||||||
Keywords | TRANSFERASE / transketolase / mycobacterium / TPP | ||||||
Function / homology | Function and homology information transketolase / transketolase activity / pentose-phosphate shunt / cell wall / extracellular region / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | ||||||
Authors | Pojer, F. / Fullam, E. / Jones, T.A. / Cole, S.T. | ||||||
Citation | Journal: Open Biol / Year: 2012 Title: Structure and function of the transketolase from Mycobacterium tuberculosis and comparison with the human enzyme. Authors: Fullam, E. / Pojer, F. / Bergfors, T. / Jones, T.A. / Cole, S.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rim.cif.gz | 529.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rim.ent.gz | 431.5 KB | Display | PDB format |
PDBx/mmJSON format | 3rim.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rim_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 3rim_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 3rim_validation.xml.gz | 104.4 KB | Display | |
Data in CIF | 3rim_validation.cif.gz | 141.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/3rim ftp://data.pdbj.org/pub/pdb/validation_reports/ri/3rim | HTTPS FTP |
-Related structure data
Related structure data | 2r8oS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 10 - 695 / Label seq-ID: 10 - 695
NCS ensembles :
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-Components
#1: Protein | Mass: 75668.562 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: tkt, Rv1449c, MT1496, MTCY493.05 / Plasmid: PET160 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: O06811, UniProt: P9WG25*PLUS, transketolase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-TPP / #4: Chemical | ChemComp-GOL / #5: 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: 2.32 Å3/Da / Density % sol: 46.88 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 17% PEG 10000, 0.1M ammonium acetate in 0.1M bis-tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 3, 2009 |
Radiation | Monochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.494→128.12 Å / Num. obs: 91429 / % possible obs: 96.62 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.49→2.64 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.77 / Num. unique all: 13701 / Rsym value: 0.431 / % possible all: 91.16 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: model of Rv1449c with E. coli transketolase (pdb entry 2r8o) as template Resolution: 2.49→19.81 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.872 / SU B: 12.779 / SU ML: 0.277 / Cross valid method: THROUGHOUT / σ(F): 2.01 / ESU R Free: 0.35 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.069 Å2
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Refinement step | Cycle: LAST / Resolution: 2.49→19.81 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.494→2.559 Å / Total num. of bins used: 20
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