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Yorodumi- PDB-3ahw: Crystal Structure of Ustilago sphaerogena Ribonuclease U2 complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ahw | ||||||
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Title | Crystal Structure of Ustilago sphaerogena Ribonuclease U2 complexed with adenosine 2'-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: 1.03 Å | ||||||
Authors | Noguchi, S. | ||||||
Citation | Journal: Protein Pept.Lett. / Year: 2010 Title: Conformational variation revealed by the crystal structure of RNase U2A complexed with Ca ion and 2'-adenylic acid at 1.03 angstrom resolution. 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 | 3ahw.cif.gz | 67.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ahw.ent.gz | 48.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ahw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/3ahw ftp://data.pdbj.org/pub/pdb/validation_reports/ah/3ahw | HTTPS FTP |
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-Related structure data
Related structure data | 3agnS 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-2AM / | ||
#3: Chemical | ChemComp-CA / #4: 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: 1.99 Å3/Da / Density % sol: 38.14 % |
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Crystal grow | Temperature: 293 K / Method: hanging drop, vapor diffusion / pH: 6.5 Details: PEG 8000, pH 6.5, hanging drop, vapor diffusion, 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 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: 1.03→37.9 Å / Num. all: 48243 / Num. obs: 47871 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 11.07 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 36.2 |
Reflection shell | Resolution: 1.03→1.057 Å / Redundancy: 3 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3554 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3AGN Resolution: 1.03→25.14 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.978 / WRfactor Rfree: 0.137 / WRfactor Rwork: 0.132 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.933 / SU B: 0.592 / SU ML: 0.014 / SU R Cruickshank DPI: 0.025 / SU Rfree: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.024 / 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: 60.02 Å2 / Biso mean: 10.729 Å2 / Biso min: 4.2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.03→25.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.03→1.057 Å / Total num. of bins used: 20
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