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- PDB-3ahw: Crystal Structure of Ustilago sphaerogena Ribonuclease U2 complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ahw | ||||||
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Title | Crystal Structure of Ustilago sphaerogena Ribonuclease U2 complexed with adenosine 2'-monophosphate | ||||||
![]() | Ribonuclease U2 | ||||||
![]() | HYDROLASE / Purine-specific endo-ribonuclease | ||||||
Function / homology | ![]() ribonuclease U2 / ribonuclease U2 activity / lyase activity / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Noguchi, S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.3 KB | Display | ![]() |
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PDB format | ![]() | 48.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 792.3 KB | Display | ![]() |
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Full document | ![]() | 793.3 KB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Data in CIF | ![]() | 12 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3agnS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() | ||
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#2: Chemical | ChemComp-2AM / | ||
#3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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