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- PDB-1zfx: The Structure of a minimal all-RNA Hairpin Ribozyme with the muta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1zfx | ||||||
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Title | The Structure of a minimal all-RNA Hairpin Ribozyme with the mutant G8U at the cleavage site | ||||||
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![]() | RNA / HAIRPIN RIBOZYME / ALL-RNA / COBALT HEXAAMINE / MUTATION / LOW SALT / S-TURN / E-LOOP / RIBOSE ZIPPER / CATALYTIC RNA | ||||||
Function / homology | COBALT HEXAMMINE(III) / RNA / RNA (> 10)![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wedekind, J.E. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.5 KB | Display | ![]() |
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PDB format | ![]() | 32.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.2 KB | Display | ![]() |
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Full document | ![]() | 447.4 KB | Display | |
Data in XML | ![]() | 4.7 KB | Display | |
Data in CIF | ![]() | 5.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1zftC ![]() 1zfvC ![]() 2bcyC ![]() 2bczC ![]() 2fgpC ![]() 2oueC ![]() 1zfr C: citing same article ( 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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Details | The asymmetric unit comprises chains A, B, C and D, which form the biological unit |
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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: 3931.408 Da / Num. of mol.: 1 / Mutation: G8U / Source method: obtained synthetically / Details: Derived from Satellite Tobacco Ringspot Virus |
#3: RNA chain | Mass: 5535.445 Da / Num. of mol.: 1 / Mutation: none / 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, 24 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/NCO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NCO.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-SO4 / | ||
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#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.95 Å3/Da / Density % sol: 68.9 % | ||||||||||||||||||||||||||||||||
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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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 30, 2004 Details: BENT TRIANGULAR ASYMMETRIC CUT SI(111) MONOCHROMATOR, RH-COATED SI MIRROR |
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: 2.38→47 Å / Num. obs: 13252 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 8.7 % / Biso Wilson estimate: 70.8 Å2 / Rsym value: 0.036 / Net I/σ(I): 29.9 |
Reflection shell | Resolution: 2.38→2.47 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 5.2 / Rsym value: 0.429 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ZFR ![]() 1zfr Resolution: 2.38→46.68 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 924127.97 / 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 THROUGHOUT
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 118.061 Å2 / ksol: 0.448302 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.38→46.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.38→2.62 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 4
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Xplor file |
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