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- PDB-2h0z: Pre-cleavage state of the Thermoanaerobacter tengcongensis glmS r... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2h0z | ||||||
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Title | Pre-cleavage state of the Thermoanaerobacter tengcongensis glmS ribozyme bound to glucose-6-phosphate | ||||||
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![]() | RNA / Ribozyme / Pseudoknot / Helix | ||||||
Function / homology | 6-O-phosphono-alpha-D-glucopyranose / : / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / RNA / RNA (> 10) / RNA (> 100)![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Klein, D.J. / Ferre-D'Amare, A.R. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.8 KB | Display | ![]() |
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PDB format | ![]() | 64.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 685.3 KB | Display | ![]() |
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Full document | ![]() | 690.3 KB | Display | |
Data in XML | ![]() | 7.2 KB | Display | |
Data in CIF | ![]() | 9.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2gcsC ![]() 2gcvC ![]() 2h0sC ![]() 2h0wC ![]() 2h0xC ![]() 2ho6C ![]() 2ho7C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly is a monomer |
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Components
#1: DNA/RNA hybrid | Mass: 8593.168 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: 40536.105 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: Sugar | ChemComp-G6P / | ||
#4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.18 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.4 Details: grown from: 12% PEG 4000, 1M LiCl, 100mM MES-NaOH pH 5.4, 5mM MgCl2. stabilized in: 24% PEG 4000, 1.5M LiCl, 30mM MgCl2, 100mM MES-NaOH pH 5.5, 20mM glucose-6-phosphate, VAPOR DIFFUSION, ...Details: grown from: 12% PEG 4000, 1M LiCl, 100mM MES-NaOH pH 5.4, 5mM MgCl2. stabilized in: 24% PEG 4000, 1.5M LiCl, 30mM MgCl2, 100mM MES-NaOH pH 5.5, 20mM glucose-6-phosphate, 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: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 26, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→99 Å / Num. all: 14171 / Num. obs: 14171 / % possible obs: 96.6 % |
Reflection shell | Resolution: 2.7→2.8 Å / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 2.7→30 Å
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Refine LS restraints |
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