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Yorodumi- PDB-2h0x: Pre-cleavage state of the Thermoanaerobacter tengcongensis glmS r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h0x | ||||||
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Title | Pre-cleavage state of the Thermoanaerobacter tengcongensis glmS ribozyme | ||||||
Components |
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Keywords | RNA / Ribozyme / Pseudoknot / Helix | ||||||
Function / homology | : / RNA / RNA (> 10) / RNA (> 100) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å | ||||||
Authors | Klein, D.J. / Ferre-D'Amare, A.R. | ||||||
Citation | Journal: Science / Year: 2006 Title: Structural basis of glmS ribozyme activation by glucosamine-6-phosphate Authors: Klein, D.J. / Ferre-D'Amare, A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h0x.cif.gz | 94.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h0x.ent.gz | 69.2 KB | Display | PDB format |
PDBx/mmJSON format | 2h0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2h0x_validation.pdf.gz | 417.2 KB | Display | wwPDB validaton report |
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Full document | 2h0x_full_validation.pdf.gz | 422.3 KB | Display | |
Data in XML | 2h0x_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 2h0x_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/2h0x ftp://data.pdbj.org/pub/pdb/validation_reports/h0/2h0x | HTTPS FTP |
-Related structure data
Related structure data | 2gcsC 2gcvC 2h0sC 2h0wC 2h0zC 2ho6C 2ho7C C: citing same article (ref.) |
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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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Details | The biological assembly is a monomer |
-Components
#1: RNA chain | Mass: 8528.203 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This sequence occurs naturally in Thermoanaerobacter tengcongensis | ||
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#2: RNA chain | Mass: 40598.070 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: RNA produced by in vitro transcription. This sequence occurs naturally in Thermoanaerobacter tengcongensis References: GenBank: 20517198 | ||
#3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.35 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 15% PEG 4000, 1M LiCl, 100mM MES-NaOH pH 5.6, 5mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||
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: 5.0.2 / Wavelength: 1.2155 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2006 |
Radiation | Monochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2155 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 22635 / Num. obs: 22635 / % possible obs: 96.3 % |
Reflection shell | Resolution: 2.3→2.38 Å / % possible all: 73.7 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.3→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: A solvent density level of 0.35 and solvent B-factor of 20 were used for the bulk solvent during refinement | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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