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Yorodumi- PDB-2gcs: Pre-cleavage state of the Thermoanaerobacter tengcongensis glmS r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gcs | ||||||
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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: 2.1 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 | 2gcs.cif.gz | 94.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gcs.ent.gz | 69.2 KB | Display | PDB format |
PDBx/mmJSON format | 2gcs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gcs_validation.pdf.gz | 413.1 KB | Display | wwPDB validaton report |
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Full document | 2gcs_full_validation.pdf.gz | 418.2 KB | Display | |
Data in XML | 2gcs_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 2gcs_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gc/2gcs ftp://data.pdbj.org/pub/pdb/validation_reports/gc/2gcs | HTTPS FTP |
-Related structure data
Related structure data | 2gcvC 2h0sC 2h0wC 2h0xC 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 the Thermoanaerobacter tengcongensis glmS ribozyme | ||
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#2: RNA chain | Mass: 40598.070 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: in vitro transcription of sequnce from 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: 2.6 Å3/Da / Density % sol: 52.72 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 14% PEG 4000, 1M LiCl, 100mM MES-NaOH pH 5.6, 5mM MgCl2, 4mM GlcN6P, 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: 5.0.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 1, 2006 |
Radiation | Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 30830 / Num. obs: 30830 / % possible obs: 99.5 % / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.1→2.18 Å / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.1→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: 2.1→30 Å
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Refine LS restraints |
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