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- PDB-2p7e: Vanadate at the Active Site of a Small Ribozyme Suggests a Role f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2p7e | ||||||
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Title | Vanadate at the Active Site of a Small Ribozyme Suggests a Role for Water in Transition-State Stabilization | ||||||
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![]() | RNA / hairpin ribozyme / vanadate / reaction intermediate / transition-state stabilization / active site waters / induced fit | ||||||
Function / homology | COBALT HEXAMMINE(III) / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / RNA / RNA (> 10)![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Torelli, A.T. / Krucinska, J. / Wedekind, J.E. | ||||||
![]() | ![]() Title: A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization Authors: Torelli, A.T. / Krucinska, J. / Wedekind, J.E. #1: ![]() 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. #2: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.5 KB | Display | ![]() |
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PDB format | ![]() | 34.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.5 KB | Display | ![]() |
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Full document | ![]() | 437.6 KB | Display | |
Data in XML | ![]() | 5.6 KB | Display | |
Data in CIF | ![]() | 7.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2p7dC ![]() 2p7fC ![]() 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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Components on special symmetry positions |
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Details | The ribozyme-substrate complex in the asymmetric unit also represents the biological unit |
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Components
-RNA chain , 2 types, 2 molecules AP
#1: RNA chain | Mass: 1587.893 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: sequence occurs naturally in tobacco ringspot virus satellite RNA |
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#5: RNA chain | Mass: 2501.553 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: sequence occurs naturally in tobacco ringspot virus satellite RNA |
-Ribozyme strand ... , 3 types, 3 molecules BCD
#2: DNA/RNA hybrid | Mass: 4182.585 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: sequence occurs naturally in tobacco ringspot virus satellite RNA |
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#3: RNA chain | Mass: 5535.445 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: sequence occurs naturally in tobacco ringspot virus satellite RNA |
#4: RNA chain | Mass: 5991.568 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: sequence occurs naturally in tobacco ringspot virus satellite RNA |
-Non-polymers , 3 types, 64 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)
#6: Chemical | ChemComp-SO4 / | ||
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#7: Chemical | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.27 Å3/Da / Density % sol: 80.57 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 250 mM Li2SO4, 2.5 mM [Co(NH3)6]Cl3, 2 mM spermidine-HCl, 4.5 mM ammonium metavanadate, 100 mM sodium cacodylate buffer and 20% PEG 2000 MME, 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 315 / Detector: CCD / Date: Apr 12, 2006 Details: Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing) |
Radiation | Monochromator: Side-scattering cuberoot I-beam bent single crystal; asymmetric cut 12.2 degs Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98789 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30.67 Å / Num. all: 21610 / Num. obs: 21610 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 5.45 % / Biso Wilson estimate: 52.6 Å2 / Rsym value: 0.046 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 4.86 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.429 / % possible all: 85.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ZFR ![]() 1zfr Resolution: 2.05→29.93 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2624271.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: Parkinson et al. Acta Cryst.D,52,57 (1996)
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.4615 Å2 / ksol: 0.316013 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→29.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 6
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Xplor file |
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