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Yorodumi- PDB-2fgp: Crystal structure of a minimal, all RNA hairpin ribozyme with mod... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fgp | ||||||
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Title | Crystal structure of a minimal, all RNA hairpin ribozyme with modifications (g8dap, u39c) at ph 8.6 | ||||||
Components |
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Keywords | RNA / RIBOZYME / G8 / DIAMINOPURINE / IN-LINE GEOMETRY / MUTANT | ||||||
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. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Crystallization and x-ray diffraction analysis of an all-rna u39c mutant of the minimal hairpin ribozyme Authors: Grum-Tokars, V. / Milovanovic, M. / 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 | 2fgp.cif.gz | 45.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fgp.ent.gz | 32.2 KB | Display | PDB format |
PDBx/mmJSON format | 2fgp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/2fgp ftp://data.pdbj.org/pub/pdb/validation_reports/fg/2fgp | HTTPS FTP |
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-Related structure data
Related structure data | 1zftC 1zfvC 1zfxC 2bcyC 2bczC 2oueC 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: 4052.470 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DERIVED FROM SATELLITE TOBACCO RINGSPOT VIRUS |
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#2: RNA chain | Mass: 3969.463 Da / Num. of mol.: 1 / Mutation: g8(N6G) / Source method: obtained synthetically / Details: DERIVED FROM SATELLITE TOBACCO RINGSPOT VIRUS |
#3: RNA chain | Mass: 5535.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DERIVED FROM SATELLITE TOBACCO RINGSPOT VIRUS |
#4: RNA chain | Mass: 5991.568 Da / Num. of mol.: 1 / Mutation: u39c / Source method: obtained synthetically / Details: DERIVED FROM SATELLITE TOBACCO RINGSPOT VIRUS |
-Non-polymers , 2 types, 8 molecules
#5: Chemical | ChemComp-NCO / |
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#6: 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: 4.14 Å3/Da / Density % sol: 70.31 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: PEG2000 MME, LITHIUM SULFATE, SPERMIDINE, COBALT HEXAMMINE, pH 8.60, 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 |
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→44.01 Å / Num. obs: 12161 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.56 % / Biso Wilson estimate: 88.1 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 34.8 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 9.25 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 5.1 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1ZFR 1zfr Resolution: 2.4→29.37 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 930166.17 / 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: 54.31 Å2 / ksol: 0.32 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 87.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→29.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.64 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 4
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Xplor file |
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