+Open data
-Basic information
Entry | Database: PDB / ID: 5fsw | ||||||
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Title | RNA dependent RNA polymerase QDE-1 from Thielavia terrestris | ||||||
Components | RNA DEPENDENT RNA POLYMERASE QDE-1 | ||||||
Keywords | TRANSFERASE / SMALL RNAS / QDE-1 ORTHOLOGUES / EVOLUTION | ||||||
Function / homology | Function and homology information regulatory ncRNA-mediated gene silencing / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / RNA binding Similarity search - Function | ||||||
Biological species | THIELAVIA TERRESTRIS (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å | ||||||
Authors | Qian, X. / Hamid, F.M. / El Sahili, A. / Darwis, D.A. / Wong, Y.H. / Bhushan, S. / Makeyev, E.V. / Lescar, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Functional Evolution in Orthologous Cell-Encoded RNA-Dependent RNA Polymerases Authors: Qian, X. / Hamid, F.M. / El Sahili, A. / Darwis, D.A. / Wong, Y.H. / Bhushan, S. / Makeyev, E.V. / Lescar, J. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN **-STRANDED BARREL THIS IS REPRESENTED BY A -9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -2-STRANDED BARREL THIS IS REPRESENTED BY A -1-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -2-STRANDED BARREL THIS IS REPRESENTED BY A -1-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -2-STRANDED BARREL THIS IS REPRESENTED BY A -1-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fsw.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5fsw.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 5fsw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/5fsw ftp://data.pdbj.org/pub/pdb/validation_reports/fs/5fsw | HTTPS FTP |
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-Related structure data
Related structure data | 2j7nS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 0 / Auth seq-ID: 22 - 1006 / Label seq-ID: 22 - 1006
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 116058.859 Da / Num. of mol.: 4 / Fragment: RDRP C-TERMINAL DOMAIN, UNP RESIDUES 364-1373 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THIELAVIA TERRESTRIS (fungus) Description: SYNTHETIC GENE FROM AEO68606.1 FROM E364 TO D1373 Plasmid: PFB-LIC-BSE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: G2R911 |
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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: 2.84 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 100 MM TRIS PH8, 75 MM NACL, 10% PEG10K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0332 |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3.19→50 Å / Num. obs: 78767 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.47 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 8.23 |
Reflection shell | Resolution: 3.19→3.38 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.14 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J7N Resolution: 3.19→48.91 Å / Cor.coef. Fo:Fc: 0.854 / Cor.coef. Fo:Fc free: 0.8 / SU B: 29.47 / SU ML: 0.256 / Cross valid method: THROUGHOUT / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.585 Å2
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Refinement step | Cycle: LAST / Resolution: 3.19→48.91 Å
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Refine LS restraints |
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