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Open data
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Basic information
Entry | Database: PDB / ID: 1nuj | ||||||
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Title | THE LEADZYME STRUCTURE BOUND TO MG(H20)6(II) AT 1.8 A RESOLUTION | ||||||
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![]() | RNA / RIBOZYME / LEADZYME / LEAD-DEPENDENT CLEAVAGE / MG(H20)62+ / BULGED NUCLEOTIDES / HYDRATED MAGNESIUM / PSEUDOHELICAL PACKING / STICKY ENDS / ALTERNATE CONFORMATION / HOMOPURINE BASE PAIRS | ||||||
Function / homology | RNA / RNA (> 10)![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Wedekind, J.E. / Mckay, D.B. | ||||||
![]() | ![]() Title: Crystal structure of the leadzyme at 1.8 A resolution: metal ion binding and the implications for catalytic mechanism and allo site ion regulation. Authors: Wedekind, J.E. / McKay, D.B. #1: ![]() Title: CRYSTAL STRUCTURE OF A LEAD DEPENDENT RIBOZYME REVEALING METAL BINDING SITES RELEVANT TO CATALYSIS Authors: Wedekind, J.E. / McKay, D.B. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75 KB | Display | ![]() |
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PDB format | ![]() | 54.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 397.1 KB | Display | ![]() |
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Full document | ![]() | 397.5 KB | Display | |
Data in XML | ![]() | 3.2 KB | Display | |
Data in CIF | ![]() | 6.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nuvC C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: RNA chain | Mass: 4194.598 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: This ribozyme was made by in vitro selection, reported by Pan & Uhlenbeck. #2: RNA chain | Mass: 3538.154 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: This ribozyme was made by in vitro selection, reported by Pan & Uhlenbeck. #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.52 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: MPD, Mg-Acetate, cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 20K | |||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 4, 1999 Details: 16 pole wiggler, Flat mirror, Si(311) bent mono with horizontal focus |
Radiation | Monochromator: si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→34 Å / Num. obs: 25779 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 26.8 Å2 / Rsym value: 0.04 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.272 / % possible all: 87.4 |
Reflection | *PLUS Lowest resolution: 34 Å / Num. obs: 25179 / Num. measured all: 286623 / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS Rmerge(I) obs: 0.272 |
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Processing
Software |
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Refinement | Method to determine structure: EXPAND TO P6(1) Starting model: NDB ENTRY UR0001 Resolution: 1.8→29.31 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.4334 Å2 / ksol: 0.287285 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.2 Å2
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Refine analyze | Luzzati coordinate error free: 0.37 Å / Luzzati sigma a free: 0.38 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→29.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 10
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 34 Å / % reflection Rfree: 8 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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