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Yorodumi- PDB-3le3: Crystal structure of apoHPr monomer from Thermoanaerobacter tengc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3le3 | ||||||
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Title | Crystal structure of apoHPr monomer from Thermoanaerobacter tengcongensis | ||||||
Components | Phosphotransferase system, HPr-related proteinsPEP group translocation | ||||||
Keywords | TRANSFERASE / HPr PTS phosphotransferase / Kinase / Phosphotransferase system | ||||||
Function / homology | Function and homology information Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / HPr-like / Histidine-containing Protein; Chain: A; / Phosphocarrier protein HPr-like / HPr-like superfamily / PTS HPr component phosphorylation site / PTS HPR domain profile. / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Thermoanaerobacter tengcongensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.861 Å | ||||||
Authors | Fu, T.M. / Su, X.D. | ||||||
Citation | Journal: To be Published Title: Dimerization of HPr by reversible domain swapping 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 | 3le3.cif.gz | 65.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3le3.ent.gz | 49.1 KB | Display | PDB format |
PDBx/mmJSON format | 3le3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/3le3 ftp://data.pdbj.org/pub/pdb/validation_reports/le/3le3 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 9620.015 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria) Strain: MB4T / Gene: FruB, TTE1820 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8R910 #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: 2.31 Å3/Da / Density % sol: 46.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.05M MgCl2, 0.1M HEPES pH7.5, 30% PEG MME 550, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9797 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 26, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→50 Å / Num. all: 23136 / Num. obs: 22049 / % possible obs: 95.3 % / Redundancy: 7.2 % / Biso Wilson estimate: 21.98 Å2 / Rsym value: 0.034 |
Reflection shell | Resolution: 1.86→1.89 Å / Redundancy: 5.8 % / Num. unique all: 1045 / % possible all: 91.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.861→30.275 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 22.12 / 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: 59.562 Å2 / ksol: 0.325 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.922 Å2
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Refinement step | Cycle: LAST / Resolution: 1.861→30.275 Å
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Refine LS restraints |
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LS refinement shell |
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