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- PDB-1m5k: Crystal structure of a hairpin ribozyme in the catalytically-acti... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1m5k | |||||||||
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Title | Crystal structure of a hairpin ribozyme in the catalytically-active conformation | |||||||||
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![]() | TRANSLATION/RNA / HAIRPIN RIBOZYME / CATALYTIC RNA / U1A RNA BINDING PROTEIN DOCKED CONFORMATION / SUBSTRATE INHIBITOR STRAND / TRANSLATION-RNA COMPLEX | |||||||||
Function / homology | ![]() U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm ...U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rupert, P.B. / Ferre-D'Amare, A.R. | |||||||||
![]() | ![]() Title: Transition state stabilization by a catalytic RNA Authors: Rupert, P.B. / Massey, A.P. / Sigurdsson, S.T. / Ferre-D'Amare, A.R. #1: ![]() Title: Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis Authors: Rupert, P.B. / Ferre-D'Amare, A.R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 181.2 KB | Display | ![]() |
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PDB format | ![]() | 135.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-RNA chain , 2 types, 4 molecules ADBE
#1: RNA chain | Mass: 6739.887 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: THIS SEQUENCE OCCURS NATURALLY IN SATELLITE TOBACCO RINGSPOT VIRUS #2: RNA chain | Mass: 29969.754 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: THIS SEQUENCE OCCURS NATURALLY IN SATELLITE TOBACCO RINGSPOT VIRUS |
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-Protein , 1 types, 2 molecules CF
#3: Protein | Mass: 11498.472 Da / Num. of mol.: 2 / Fragment: U1A RNA BINDING DOMAIN / Mutation: Y31H,Q36R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 3 types, 138 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CA / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.78 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 5 Details: MPD, ammonium chloride, calcium chloride, pH 5.0, VAPOR DIFFUSION, SITTING DROP at 300K, VAPOR DIFFUSION, SITTING DROP | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion / Details: Rupert, P.B., (2001) Nature, 410, 780. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 5, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→61.07 Å / Num. all: 41156 / Num. obs: 41156 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 43.2 Å2 / Rsym value: 0.067 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3147 / % possible all: 73.9 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 100 Å / Num. obs: 41290 / % possible obs: 95.6 % / Rmerge(I) obs: 0.067 |
Reflection shell | *PLUS % possible obs: 73.9 % / Rmerge(I) obs: 0.261 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: Engh & Huber, Parkinson et al.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.68 Å2 / ksol: 0.275 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 86.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→61.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor obs: 0.23 / Rfactor Rfree: 0.285 / Rfactor Rwork: 0.229 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.41 / Rfactor Rwork: 0.376 |