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Yorodumi- PDB-4ieg: Structure and interactions of the RNA-dependent RNA polymerase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ieg | ||||||
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Title | Structure and interactions of the RNA-dependent RNA polymerase from bacteriophage phi12 (P1 crystal form) | ||||||
Components | RNA-dependent RNA polymerase P2 | ||||||
Keywords | TRANSFERASE / RNA-directed RNA polymerase | ||||||
Function / homology | Cystovirus, RNA-directed RNA polymerase / RNA-directed RNA polymerase, bacteriophage, catalytic domain / RdRp of RNA-containing bacteriophages catalytic domain profile. / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA/RNA polymerase superfamily / metal ion binding / RNA-directed RNA polymerase Function and homology information | ||||||
Biological species | Pseudomonas phage phi12 (bacteriophage) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Ren, Z. / Franklin, M.C. / Ghose, R. | ||||||
Citation | Journal: Proteins / Year: 2013 Title: Structure of the RNA-directed RNA Polymerase from the cystovirus 12. Authors: Ren, Z. / C Franklin, M. / Ghose, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ieg.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4ieg.ent.gz | 869.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ieg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ieg_validation.pdf.gz | 454.9 KB | Display | wwPDB validaton report |
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Full document | 4ieg_full_validation.pdf.gz | 476.9 KB | Display | |
Data in XML | 4ieg_validation.xml.gz | 103 KB | Display | |
Data in CIF | 4ieg_validation.cif.gz | 150 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/4ieg ftp://data.pdbj.org/pub/pdb/validation_reports/ie/4ieg | HTTPS FTP |
-Related structure data
Related structure data | 4gzkSC 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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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: 75460.359 Da / Num. of mol.: 4 / Mutation: M2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas phage phi12 (bacteriophage) Gene: P2 / Plasmid: pPG27 / Production host: Escherichia coli (E. coli) / Strain (production host): BL12(DE3) / References: UniProt: Q94M06 #2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | |
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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: 2.29 Å3/Da / Density % sol: 46.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M Mg formate 20% PEG 3350, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 3, 2012 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 156487 / Num. obs: 144893 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 2.9 / Num. unique all: 7802 / % possible all: 87.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4GZK Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.882 / SU B: 14.902 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.329 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.467 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.15 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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