[English] 日本語
Yorodumi- PDB-3agn: Crystal Structure of Ustilago sphaerogena Ribonuclease U2 Complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3agn | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Ustilago sphaerogena Ribonuclease U2 Complexed with adenosine 3'-monophosphate | ||||||
Components | Ribonuclease U2 | ||||||
Keywords | HYDROLASE / purine-specific endo-ribonuclease | ||||||
Function / homology | Function and homology information ribonuclease U2 / ribonuclease U2 activity / lyase activity / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Ustilago sphaerogena (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.96 Å | ||||||
Authors | Noguchi, S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2010 Title: Isomerization mechanism of aspartate to isoaspartate implied by structures of Ustilago sphaerogena ribonuclease U2 complexed with adenosine 3'-monophosphate Authors: Noguchi, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3agn.cif.gz | 66.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3agn.ent.gz | 47.7 KB | Display | PDB format |
PDBx/mmJSON format | 3agn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3agn_validation.pdf.gz | 999.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3agn_full_validation.pdf.gz | 999.7 KB | Display | |
Data in XML | 3agn_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 3agn_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/3agn ftp://data.pdbj.org/pub/pdb/validation_reports/ag/3agn | HTTPS FTP |
-Related structure data
Related structure data | 3agoC 1rtuS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 12392.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ustilago sphaerogena (fungus) / References: UniProt: P00654, EC: 3.1.27.4 |
---|---|
#2: Chemical | ChemComp-3AM / [( |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.81 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.75 Details: 12.5% PEG 8000, 200mM calcium acetate, 100mM sodium cacodylate, 240mM HCl, pH 3.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Jan 25, 2010 |
Radiation | Monochromator: TRIANGULAR Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 0.96→34.3 Å / Num. obs: 58543 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 14.7 % / Biso Wilson estimate: 8 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 72.2 |
Reflection shell | Resolution: 0.96→0.984 Å / Redundancy: 5 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 7.43 / Num. unique all: 3749 / % possible all: 86.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RTU Resolution: 0.96→31.05 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.975 / WRfactor Rfree: 0.125 / WRfactor Rwork: 0.116 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.954 / SU B: 0.336 / SU ML: 0.009 / SU R Cruickshank DPI: 0.018 / SU Rfree: 0.018 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.018 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 48.82 Å2 / Biso mean: 6.48 Å2 / Biso min: 2.73 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.96→31.05 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 0.959→0.984 Å / Total num. of bins used: 20
|