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Yorodumi- PDB-2bcz: Crystal Structure of a minimal, mutant all-RNA hairpin ribozyme (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bcz | ||||||
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Title | Crystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8I, 2'deoxy A-1) | ||||||
Components |
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Keywords | RNA / ribozyme / G8 / inosine | ||||||
Function / homology | COBALT HEXAMMINE(III) / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å | ||||||
Authors | Salter, J.D. / Wedekind, J.E. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Water in the Active Site of an All-RNA Hairpin Ribozyme and Effects of Gua8 Base Variants on the Geometry of Phosphoryl Transfer. Authors: Salter, J.D. / Krucinska, J. / Alam, S. / Grum-Tokars, V. / Wedekind, J.E. #1: Journal: Biochemistry / Year: 2005 Title: Conformational Heterogeneity at Position U37 of an All-RNA Hairpin Ribozyme with Implications for Metal Binding and the Catalytic Structure of the S-Turn Authors: Alam, S. / Grum-Tokars, V. / Krucinska, J. / Kundracik, M.L. / 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 | 2bcz.cif.gz | 45.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bcz.ent.gz | 31.8 KB | Display | PDB format |
PDBx/mmJSON format | 2bcz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bcz_validation.pdf.gz | 436.5 KB | Display | wwPDB validaton report |
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Full document | 2bcz_full_validation.pdf.gz | 439.4 KB | Display | |
Data in XML | 2bcz_validation.xml.gz | 4.5 KB | Display | |
Data in CIF | 2bcz_validation.cif.gz | 5.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/2bcz ftp://data.pdbj.org/pub/pdb/validation_reports/bc/2bcz | HTTPS FTP |
-Related structure data
Related structure data | 1zftC 1zfvC 1zfxC 2bcyC 2fgpC 2oueC 1zfr 2bb1 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: 4036.471 Da / Num. of mol.: 1 / Mutation: A1(DA) / Source method: obtained synthetically |
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#2: RNA chain | Mass: 3955.433 Da / Num. of mol.: 1 / Mutation: G8I / Source method: obtained synthetically |
#3: RNA chain | Mass: 5535.445 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: RNA chain | Mass: 5991.568 Da / Num. of mol.: 1 / Mutation: U39C / Source method: obtained synthetically |
-Non-polymers , 3 types, 8 molecules
#5: Chemical | ChemComp-SO4 / | ||
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#6: Chemical | #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: 4.21 Å3/Da / Density % sol: 70.79 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: PEG550 MME, lithium sulfate, spermidine, cobalt hexamine, , pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 83 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9764 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 5, 2005 |
Radiation | Monochromator: bent triangular asymmetric cut si(111) monochromator, RH-coated si for vertical focussing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9764 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→44.3 Å / Num. all: 13689 / Num. obs: 13689 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.25 % / Biso Wilson estimate: 104.9 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 2.4→2.48 Å / Redundancy: 5.91 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.3 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 1ZFR 1zfr Resolution: 2.4→44.3 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1771956.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: CNS v1.1
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 75.3413 Å2 / ksol: 0.319713 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→44.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.64 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 4
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Xplor file |
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