+Open data
-Basic information
Entry | Database: PDB / ID: 2dfh | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Tk-RNase HII(1-212)-C | ||||||
Components | Ribonuclease HII | ||||||
Keywords | HYDROLASE / Chameleon sequence / ribonuclease HII / Thermococcus kodakaraensis / fusion protein | ||||||
Function / homology | Function and homology information ribonuclease H2 complex / DNA replication, removal of RNA primer / ribonuclease H / mismatch repair / RNA-DNA hybrid ribonuclease activity / manganese ion binding / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermococcus kodakarensis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | ||||||
Authors | Katagiri, Y. / Takano, K. / Chon, H. / Matsumura, H. / Koga, Y. / Kanaya, S. | ||||||
Citation | Journal: Proteins / Year: 2007 Title: Conformational contagion in a protein: Structural properties of a chameleon sequence Authors: Takano, K. / Katagiri, Y. / Mukaiyama, A. / Chon, H. / Matsumura, H. / Koga, Y. / Kanaya, S. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE The C-terminal 9 residues, TQDMINKST are chameleon sequencein. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2dfh.cif.gz | 58.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2dfh.ent.gz | 42 KB | Display | PDB format |
PDBx/mmJSON format | 2dfh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/2dfh ftp://data.pdbj.org/pub/pdb/validation_reports/df/2dfh | HTTPS FTP |
---|
-Related structure data
Related structure data | 2df5C 2dfeC 2dffC 2dfiC 1io2S 2dfg S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a monomer generated from the monomer in the asymmetric unit. |
-Components
#1: Protein | Mass: 24865.410 Da / Num. of mol.: 1 / Mutation: chameleon sequence Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Plasmid: pJAL700K-C04 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: O74035, ribonuclease H |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.74 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 10% PEG 8000, 0.2M MES, 20% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 18, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→50 Å / Num. obs: 9466 / % possible obs: 98.9 % / Biso Wilson estimate: 13.6 Å2 |
Reflection shell | Resolution: 2.27→2.35 Å / % possible all: 91.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IO2 Resolution: 2.27→26.12 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1546820.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.5838 Å2 / ksol: 0.381132 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.7 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.27→26.12 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.27→2.41 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|