[English] 日本語
Yorodumi- PDB-3i67: Ribonuclease A by LB nanotemplate method after high X-Ray dose on... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i67 | ||||||
---|---|---|---|---|---|---|---|
Title | Ribonuclease A by LB nanotemplate method after high X-Ray dose on ESRF ID14-2 beamline | ||||||
Components | Ribonuclease pancreaticPancreatic ribonuclease family | ||||||
Keywords | HYDROLASE / Ribonuclease A / Disulfide bond / Endonuclease / Glycation / Glycoprotein / Nuclease / Secreted | ||||||
Function / homology | Function and homology information pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å | ||||||
Authors | Pechkova, E. / Tripathi, S.K. / Ravelli, R. / McSweeney, S. / Nicolini, C. | ||||||
Citation | Journal: To be Published Title: Atomic structure and radiation resistance of langmuir-blodgett protein crystals Authors: Pechkova, E. / McSweeney, S. / Nicolini, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3i67.cif.gz | 63.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3i67.ent.gz | 46.4 KB | Display | PDB format |
PDBx/mmJSON format | 3i67.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/3i67 ftp://data.pdbj.org/pub/pdb/validation_reports/i6/3i67 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3i6fC 3i6hC 3i6jC 2blpS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: Pancreas / References: UniProt: P61823, EC: 3.1.27.5 |
---|---|
#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.66 % / Mosaicity: 0.46 ° |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.75M ammonium sulphate, 2.0M Sodium Chloride, 100mM Na-acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 1.3 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 14, 2007 / Details: mirror |
Radiation | Monochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→55.728 Å / Num. obs: 37910 / % possible obs: 100 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.14 / Rsym value: 0.14 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 0.3 / Num. measured all: 28424 / Num. unique all: 5449 / Rsym value: 0.2392 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BLP Resolution: 1.3→55.728 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.203 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.848 / SU B: 1.983 / SU ML: 0.043 / SU R Cruickshank DPI: 0.061 / SU Rfree: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 43.53 Å2 / Biso mean: 16.645 Å2 / Biso min: 6.2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→55.728 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.3→1.334 Å / Total num. of bins used: 20
|