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Yorodumi- PDB-2npy: Crystal Structure of a junctioned hairpin ribozyme incorporating ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2npy | ||||||
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Title | Crystal Structure of a junctioned hairpin ribozyme incorporating 9atom linker and 2'-deoxy 2'-amino U at A-1 | ||||||
Components |
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Keywords | RNA / HAIRPIN RIBOZYME / MUTATION / S-TURN / E-LOOP / RIBOSE ZIPPER / CATALYTIC RNA / 2'-deoxy 2'-amino / 9S linker | ||||||
Function / homology | COBALT HEXAMMINE(III) / Chem-S9L / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.65 Å | ||||||
Authors | MacElrevey, C. / Krucinska, J. / Wedekind, J.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme. Authors: MacElrevey, C. / Spitale, R.C. / Krucinska, J. / Wedekind, J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2npy.cif.gz | 42.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2npy.ent.gz | 32.3 KB | Display | PDB format |
PDBx/mmJSON format | 2npy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2npy_validation.pdf.gz | 441.9 KB | Display | wwPDB validaton report |
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Full document | 2npy_full_validation.pdf.gz | 442.4 KB | Display | |
Data in XML | 2npy_validation.xml.gz | 4.6 KB | Display | |
Data in CIF | 2npy_validation.cif.gz | 5.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/2npy ftp://data.pdbj.org/pub/pdb/validation_reports/np/2npy | HTTPS FTP |
-Related structure data
Related structure data | 2npzC 1zfr 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
-RNA chain , 4 types, 4 molecules ABCD
#1: RNA chain | Mass: 4028.446 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Sequence occurs naturally in satellite RNA tobacco ringspot virus |
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#2: RNA chain | Mass: 3970.448 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Sequence occurs naturally in satellite RNA tobacco ringspot virus |
#3: RNA chain | Mass: 5535.445 Da / Num. of mol.: 1 / Fragment: S-TURN STRAND / Mutation: U39C / Source method: obtained synthetically Details: Sequence occurs naturally in satellite RNA tobacco ringspot virus |
#4: RNA chain | Mass: 5991.568 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Sequence occurs naturally in satellite RNA tobacco ringspot virus |
-Non-polymers , 3 types, 16 molecules
#5: Chemical | ChemComp-NCO / |
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#6: Chemical | ChemComp-S9L / |
#7: 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: 4.3 Å3/Da / Density % sol: 80.5 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: PEG 2000 MME, lithium sulfate, cacodylate, spermidine, cobalt hexaamine, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 31, 2005 Details: bent triangular asymmetric cut SI (111) (horizontal), RH coated SI mirror (vertical) |
Radiation | Monochromator: BENT TRIANGULAR ASYMMETRIC CUT SI(111) MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→38.98 Å / Num. all: 10537 / Num. obs: 10389 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 15.3 % / Biso Wilson estimate: 84 Å2 / Rsym value: 0.059 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 2.65→2.74 Å / Redundancy: 16.1 % / Mean I/σ(I) obs: 6 / Num. unique all: 1006 / Rsym value: 0.457 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1ZFR 1zfr Resolution: 2.65→30.42 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 644495.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(I): -3 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.9902 Å2 / ksol: 0.308956 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.65→30.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.92 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 4
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Xplor file |
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