+Open data
-Basic information
Entry | Database: PDB / ID: 7kju | ||||||
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Title | Cgi121-tRNA complex | ||||||
Components | RNA (75-MER) | ||||||
Keywords | RNA / KEOPS / tRNA / Cgi121 / RNA modifying enzyme / N6-threonylcarbamoyl adenosine | ||||||
Function / homology | : / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.102 Å | ||||||
Authors | Ceccarelli, D.F. / Beenstock, J. / Wan, L.C.K. / Sicheri, F. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Nat Commun / Year: 2020 Title: A substrate binding model for the KEOPS tRNA modifying complex. Authors: Beenstock, J. / Ona, S.M. / Porat, J. / Orlicky, S. / Wan, L.C.K. / Ceccarelli, D.F. / Maisonneuve, P. / Szilard, R.K. / Yin, Z. / Setiaputra, D. / Mao, D.Y.L. / Khan, M. / Raval, S. / ...Authors: Beenstock, J. / Ona, S.M. / Porat, J. / Orlicky, S. / Wan, L.C.K. / Ceccarelli, D.F. / Maisonneuve, P. / Szilard, R.K. / Yin, Z. / Setiaputra, D. / Mao, D.Y.L. / Khan, M. / Raval, S. / Schriemer, D.C. / Bayfield, M.A. / Durocher, D. / Sicheri, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kju.cif.gz | 113 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kju.ent.gz | 88.9 KB | Display | PDB format |
PDBx/mmJSON format | 7kju.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kju_validation.pdf.gz | 400 KB | Display | wwPDB validaton report |
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Full document | 7kju_full_validation.pdf.gz | 401 KB | Display | |
Data in XML | 7kju_validation.xml.gz | 4.1 KB | Display | |
Data in CIF | 7kju_validation.cif.gz | 5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kj/7kju ftp://data.pdbj.org/pub/pdb/validation_reports/kj/7kju | HTTPS FTP |
-Related structure data
Related structure data | 7kjtC 3l0uS S: Starting model for refinement 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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-Components
#1: RNA chain | Mass: 24413.467 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Plasmid: pUC19 / Details (production host): hepatitis delta virus ribozyme Production host: in vitro transcription vector pT7-Fluc(deltai) (others) References: GenBank: 6626255 | ||
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#2: Chemical | ChemComp-MG / Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.98 Å3/Da / Density % sol: 79.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM MES, pH 6.0, 0.2 M zinc acetate, 10% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97964 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 21, 2013 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97964 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.1→49.14 Å / Num. obs: 10895 / % possible obs: 99.9 % / Redundancy: 11.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.025 / Rrim(I) all: 0.085 / Net I/σ(I): 13.3 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3L0U Resolution: 3.102→49.034 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 42.19 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 432.37 Å2 / Biso mean: 181.6269 Å2 / Biso min: 37.96 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.102→49.034 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -32.618 Å / Origin y: -10.6402 Å / Origin z: 10.417 Å
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Refinement TLS group | Selection details: (chain 'A' and resid 1 through 75) |