[English] 日本語
Yorodumi- PDB-3lfg: Crystal structure of HPr-C-His from Thermoanaerobacter tengcongensis -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lfg | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of HPr-C-His from Thermoanaerobacter tengcongensis | ||||||
Components | Phosphotransferase system, HPr-related proteins | ||||||
Keywords | TRANSFERASE / HPr fruB phosphotransfer PTS / 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: 1.58 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3lfg.cif.gz | 115.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3lfg.ent.gz | 91.1 KB | Display | PDB format |
PDBx/mmJSON format | 3lfg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lfg_validation.pdf.gz | 440.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3lfg_full_validation.pdf.gz | 441.5 KB | Display | |
Data in XML | 3lfg_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 3lfg_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/3lfg ftp://data.pdbj.org/pub/pdb/validation_reports/lf/3lfg | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 10691.167 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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.01 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 30% PEG 4000, 0.1M NaAc pH 4.6, 0.2M ammonium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.9798 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 2, 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: 1.58→50 Å / Num. all: 37529 / Num. obs: 37192 / % possible obs: 99.1 % / Redundancy: 7.6 % / Biso Wilson estimate: 17.36 Å2 / Rsym value: 0.116 |
Reflection shell | Resolution: 1.58→1.61 Å / Redundancy: 4.7 % / Num. unique all: 1683 / % possible all: 91.4 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→28.16 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.863 / SU ML: 0.23 / σ(F): 1.34 / Phase error: 19.87 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.793 Å2 / ksol: 0.383 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.92 Å2 / Biso mean: 19.972 Å2 / Biso min: 8.63 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→28.16 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 11.16 Å / Origin y: -10.8294 Å / Origin z: 11.0281 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|