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Yorodumi- PDB-1zfv: The structure of an all-RNA minimal Hairpin Ribozyme with Mutatio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zfv | ||||||
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Title | The structure of an all-RNA minimal Hairpin Ribozyme with Mutation G8A at the cleavage site | ||||||
Components |
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Keywords | RNA / HAIRPIN RIBOZYME / ALL-RNA / COBALT HEXAAMINE / MUTATION / JUNCTIONLESS / LOW SALT / S-TURN / E-LOOP / RIBOSE ZIPPER / CATALYTIC RNA | ||||||
Function / homology | COBALT HEXAMMINE(III) / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å | ||||||
Authors | 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. / Krucinska, J. / Alam, S. / Grum-Tokars, V. / Wedekind, J.E. #1: 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. #2: Journal: Embo J. / Year: 2001 Title: Functional involvement of G8 in the hairpin ribozyme cleavage mechanism Authors: Pinard, R. / Hampel, K.J. / Heckman, J.E. / Lambert, D. / Chan, P.A. / Major, F. / Burke, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zfv.cif.gz | 45.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zfv.ent.gz | 32.5 KB | Display | PDB format |
PDBx/mmJSON format | 1zfv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zfv_validation.pdf.gz | 443.5 KB | Display | wwPDB validaton report |
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Full document | 1zfv_full_validation.pdf.gz | 446.7 KB | Display | |
Data in XML | 1zfv_validation.xml.gz | 5.1 KB | Display | |
Data in CIF | 1zfv_validation.cif.gz | 6.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/1zfv ftp://data.pdbj.org/pub/pdb/validation_reports/zf/1zfv | HTTPS FTP |
-Related structure data
Related structure data | 1zftC 1zfxC 2bcyC 2bczC 2fgpC 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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Details | The asymmetric unit comprises strands A, B, C and D, which form the biological unit |
-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: 3954.448 Da / Num. of mol.: 1 / Mutation: G8A / 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 , 3 types, 36 molecules
#5: Chemical | ChemComp-SO4 / |
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#6: Chemical | ChemComp-NCO / |
#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 Å3/Da / Density % sol: 69.2 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 2000 MME, LITHIUM SULFATE, SPERMIDINE, COBALT HEXAAMINE , pH 6.0, 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: 0.978 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 29, 2004 Details: BENT TRIANGULAR ASYMMETRIC CUT SI(111) MONOCHROMATOR (PROVIDES HORIZONTAL FOCUSING), RH-COATED SI MIRROR FOR VERTICAL FOCUSSING |
Radiation | Monochromator: BENT TRIANGULAR ASYMMETRIC CUT SI(111) MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→44 Å / Num. obs: 13112 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 11.9 % / Biso Wilson estimate: 74.3 Å2 / Rsym value: 0.045 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 11 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.428 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1ZFR 1zfr Resolution: 2.4→43.77 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1305392.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -5 / Stereochemistry target values: CNS / Details: MLI TARGET USED THROUGHOUT
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.2932 Å2 / ksol: 0.349546 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→43.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.64 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 4
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Xplor file |
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