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Yorodumi- PDB-3ago: Crystal Structure of Ustilago sphaerogena Ribonuclease U2 complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ago | ||||||
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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: 0.99 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ago.cif.gz | 63.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ago.ent.gz | 45.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ago.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/3ago ftp://data.pdbj.org/pub/pdb/validation_reports/ag/3ago | HTTPS FTP |
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-Related structure data
Related structure data | 3agnC 1rtuS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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 | ||||
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#2: Chemical | ChemComp-3AM / [( | ||||
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.6464 Å3/Da / Density % sol: 25.2916 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Jan 1, 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: 0.99→34.3 Å / Num. obs: 43053 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 9.8 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 58 |
Reflection shell | Resolution: 0.99→1.02 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 6.6 / Num. unique all: 3011 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RTU Resolution: 0.99→32.71 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.976 / WRfactor Rfree: 0.16 / WRfactor Rwork: 0.147 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.915 / SU B: 0.655 / SU ML: 0.016 / SU R Cruickshank DPI: 0.027 / SU Rfree: 0.026 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.028 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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: 40.26 Å2 / Biso mean: 9.168 Å2 / Biso min: 4.22 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 0.99→32.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.99→1.016 Å / Total num. of bins used: 20
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