+Open data
-Basic information
Entry | Database: PDB / ID: 3lfh | ||||||
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Title | Crystal structure of manxA from Thermoanaerobacter tengcongensis | ||||||
Components | Phosphotransferase system, mannose/fructose-specific component IIAPEP group translocation | ||||||
Keywords | TRANSFERASE / manxA / PTS | ||||||
Function / homology | Function and homology information phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / phosphorylation / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Thermoanaerobacter tengcongensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.805 Å | ||||||
Authors | Fu, T.M. / Su, X.-D. | ||||||
Citation | Journal: To be Published Title: Crystal structure of manxA and manxB from Thermoanaerobacter tengcongensis Authors: Fu, T.M. / Su, X.-D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lfh.cif.gz | 167 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lfh.ent.gz | 132.7 KB | Display | PDB format |
PDBx/mmJSON format | 3lfh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/3lfh ftp://data.pdbj.org/pub/pdb/validation_reports/lf/3lfh | HTTPS FTP |
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-Related structure data
Related structure data | 3lfjC 1pdoS C: citing same article (ref.) 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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-Components
#1: Protein | Mass: 16205.996 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria) Strain: MB4T / Gene: manxA / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8RD55 #2: 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: 1.97 Å3/Da / Density % sol: 37.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Bis-Tris pH 6.5, 45% PPG P400, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9798 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 6, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 69004 / Num. obs: 68659 / % possible obs: 99.5 % / Redundancy: 5.2 % / Biso Wilson estimate: 29.83 Å2 / Rsym value: 0.093 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 5.1 % / Num. unique all: 3450 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1pdo Resolution: 1.805→40.945 Å / Occupancy max: 1 / Occupancy min: 0.14 / FOM work R set: 0.846 / SU ML: 0.23 / σ(F): 1.36 / Phase error: 22.76 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.762 Å2 / ksol: 0.365 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.84 Å2 / Biso mean: 37.123 Å2 / Biso min: 18.61 Å2
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Refinement step | Cycle: LAST / Resolution: 1.805→40.945 Å
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Refine LS restraints |
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LS refinement shell |
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