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Yorodumi- PDB-2czj: Crystal structure of the tRNA domain of tmRNA from Thermus thermo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2czj | ||||||
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Title | Crystal structure of the tRNA domain of tmRNA from Thermus thermophilus HB8 | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / SmpB / tmRNA / SsrA RNA / 10Sa RNA / tRNA / trans-translation / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / RNA BINDING PROTEIN-RNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å | ||||||
Authors | Bessho, Y. / Shibata, R. / Sekine, S. / Murayama, K. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA. Authors: Bessho, Y. / Shibata, R. / Sekine, S. / Murayama, K. / Higashijima, K. / Hori-Takemoto, C. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2czj.cif.gz | 240.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2czj.ent.gz | 189.2 KB | Display | PDB format |
PDBx/mmJSON format | 2czj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2czj_validation.pdf.gz | 444.2 KB | Display | wwPDB validaton report |
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Full document | 2czj_full_validation.pdf.gz | 586.7 KB | Display | |
Data in XML | 2czj_validation.xml.gz | 35.1 KB | Display | |
Data in CIF | 2czj_validation.cif.gz | 50.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/2czj ftp://data.pdbj.org/pub/pdb/validation_reports/cz/2czj | HTTPS FTP |
-Related structure data
Related structure data | 1wjxSC 1p6vS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-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: Protein | Mass: 14177.479 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RR57 #2: RNA chain | Mass: 20289.061 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: Total 63nt of RNA was generated by binding T7 trascript (41nt) and chemically synthesized RNA (22nt). |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 66.4 % | ||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: HEPES, ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 14, 2004 |
Radiation | Monochromator: double flat Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.01→48.76 Å / Num. obs: 40370 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.33 % / Rsym value: 0.075 / Net I/σ(I): 23.69 |
Reflection shell | Resolution: 3.01→3.11 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 3977 / Rsym value: 0.366 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1P6V, 1WJX Resolution: 3.01→48.76 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: THIS CRYSTAL HAS A PSEUDO-MEROHEDRAL PERFECT TWINNING. THE TWINNING OPERATER IS (H,K,L) -> (H,-K,-L). THE R-FACTOR IS 0.255 AND THE R-FREE IS 0.320 WHEN THIS TWINING OPERATOR IS USED WITH TWIN_LSQ TARGET.
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Displacement parameters | Biso mean: 94.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.01→48.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.14 Å / Rfactor Rfree: 0.375 / Rfactor Rwork: 0.361 / Total num. of bins used: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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