+Open data
-Basic information
Entry | Database: PDB / ID: 1muk | ||||||
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Title | reovirus lambda3 native structure | ||||||
Components | MINOR CORE PROTEIN LAMBDA 3 | ||||||
Keywords | VIRAL PROTEIN / single subunit polymerase fold / fingers / palm / thumb / right hand configuration | ||||||
Function / homology | Function and homology information viral genome replication / viral nucleocapsid / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / RNA binding Similarity search - Function | ||||||
Biological species | Reovirus sp. | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR, MAD / Resolution: 2.5 Å | ||||||
Authors | Tao, Y. / Farsetta, D.L. / Nibert, M.L. / Harrison, S.C. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2002 Title: RNA Synthesis in a Cage-Structural Studies of Reovirus Polymerase lambda3 Authors: Tao, Y. / Farsetta, D.L. / Nibert, M.L. / Harrison, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1muk.cif.gz | 269.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1muk.ent.gz | 213.5 KB | Display | PDB format |
PDBx/mmJSON format | 1muk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mu/1muk ftp://data.pdbj.org/pub/pdb/validation_reports/mu/1muk | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 142423.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Reovirus sp. / Strain: T3D / Gene: L1 / Cell line (production host): SF21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P17378, UniProt: P0CK31*PLUS |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.28 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: PEG4000, sodium chloride, HEPES, glycerol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→42.94 Å / Num. all: 52366 / Num. obs: 52366 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 6 % / Biso Wilson estimate: 32 Å2 / Limit h max: 28 / Limit h min: 0 / Limit k max: 34 / Limit k min: 0 / Limit l max: 99 / Limit l min: 0 / Observed criterion F max: 2477003.57 / Observed criterion F min: 11.3 / Rmerge(I) obs: 0.069 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 4.7 / Num. unique all: 4487 / % possible all: 85 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 30 Å / Num. obs: 52430 / Num. measured all: 337229 |
Reflection shell | *PLUS % possible obs: 85 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR, MAD / Resolution: 2.5→42.94 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 21.5153 Å2 / ksol: 0.334817 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.88 Å2 / Biso mean: 23.68 Å2 / Biso min: 2.71 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→42.94 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.245 / Rfactor Rwork: 0.213 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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