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Yorodumi- PDB-3dhs: Mapping metal-binding sites in the catalytic domain of bacterial ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dhs | ||||||
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Title | Mapping metal-binding sites in the catalytic domain of bacterial RNase P RNA | ||||||
Components | RNase P RNA | ||||||
Keywords | HYDROLASE / RNA / CATALYTIC RNA / RNA PROCESSING | ||||||
Function / homology | OSMIUM ION / RNA / RNA (> 10) / RNA (> 100) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / SAD / molecular replacement / Resolution: 3.6 Å | ||||||
Authors | Pace, N.R. / Kazantsev, A.V. / Krivenko, A.A. | ||||||
Citation | Journal: Rna / Year: 2009 Title: Mapping metal-binding sites in the catalytic domain of bacterial RNase P RNA Authors: Kazantsev, A.V. / Krivenko, A.A. / Pace, N.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dhs.cif.gz | 117.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dhs.ent.gz | 86.2 KB | Display | PDB format |
PDBx/mmJSON format | 3dhs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dhs_validation.pdf.gz | 377.1 KB | Display | wwPDB validaton report |
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Full document | 3dhs_full_validation.pdf.gz | 389.9 KB | Display | |
Data in XML | 3dhs_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 3dhs_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/3dhs ftp://data.pdbj.org/pub/pdb/validation_reports/dh/3dhs | HTTPS FTP |
-Related structure data
Related structure data | 2a64S 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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-Components
#1: RNA chain | Mass: 87003.711 Da / Num. of mol.: 1 / Fragment: Catalytic domain / Source method: obtained synthetically Details: RNA was prepared by in vitro transcription and is naturally found in Bacillus stearothermophilus. References: ribonuclease P |
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#2: Chemical | ChemComp-OS / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.52 Å3/Da / Density % sol: 72.79 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.05 M cacodylate, 0.1 M potassium chloride, 0.02 M magnesium chloride, 0.001 M spermine tetrachloride, 23% 1,6-hexanediol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.1401 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 2, 2004 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1401 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 13.64 % / Av σ(I) over netI: 10.2 / Number: 252493 / Rmerge(I) obs: 0.102 / Χ2: 1 / D res high: 3.6 Å / D res low: 42.07 Å / Num. obs: 18374 / % possible obs: 98.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell | ID: 1
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Reflection | Resolution: 3.6→42.07 Å / Num. obs: 18374 / % possible obs: 98.7 % / Redundancy: 13.64 % / Rmerge(I) obs: 0.102 / Χ2: 1 / Net I/σ(I): 10.2 / Scaling rejects: 1894 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 3.6→3.73 Å / Redundancy: 13.66 % / Rmerge(I) obs: 0.714 / Mean I/σ(I) obs: 2.9 / Num. measured all: 24484 / Num. unique all: 1786 / Χ2: 1.17 / % possible all: 98.6 |
-Phasing
Phasing |
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Phasing MR | Method translation: &STRIP%trans_method | |||
Phasing dm shell | Resolution: 3.6→500.01 Å / Delta phi final: 0.154 / FOM : 0.165 / Reflection: 34294 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2a64 Resolution: 3.6→42.07 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.69 / Data cutoff high absF: 2541105 / Data cutoff low absF: 0 / Isotropic thermal model: ANISOTROPIC, GROUP / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman, Acta Cryst. D, 52, 57-64 (1996) Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46 Å2 / ksol: 0.1 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 462.91 Å2 / Biso mean: 209.908 Å2 / Biso min: 17.98 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.6→42.07 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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Xplor file |
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