+Open data
-Basic information
Entry | Database: PDB / ID: 1n35 | ||||||
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Title | lambda3 elongation complex with four phosphodiester bond formed | ||||||
Components |
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Keywords | TRANSFERASE/RNA / RNA polymerase / right hand configuration / bracelet / TRANSFERASE-RNA COMPLEX | ||||||
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 | Mammalian orthoreovirus 3 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 [lambda] 3 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 | 1n35.cif.gz | 280.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n35.ent.gz | 218.9 KB | Display | PDB format |
PDBx/mmJSON format | 1n35.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/1n35 ftp://data.pdbj.org/pub/pdb/validation_reports/n3/1n35 | 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
-RNA chain , 2 types, 2 molecules BC
#1: RNA chain | Mass: 1681.072 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: RNA chain | Mass: 3096.901 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: AUUAGC, Ordered from Dharmacon |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 142423.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mammalian orthoreovirus 3 / Genus: Orthoreovirus / Species: Mammalian orthoreovirus / Strain: Dearing / Gene: L1 / Plasmid: pFastbac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF21 / References: UniProt: P17378, UniProt: P0CK31*PLUS |
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-Non-polymers , 3 types, 355 molecules
#4: Chemical | #5: Chemical | #6: 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: 2.55 Å3/Da / Density % sol: 51.77 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: PEG4000, NaCl, HEPES, glycerol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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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: CHESS / Beamline: F1 / Wavelength: 0.948 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 20, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.948 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 48139 / Num. obs: 48139 / % possible obs: 89.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3.5 % / Biso Wilson estimate: 46 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2 / Num. unique all: 3986 / % possible all: 75.3 |
Reflection | *PLUS Lowest resolution: 30 Å / Redundancy: 3-4 |
Reflection shell | *PLUS % possible obs: 75.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: lambda3 native structure Resolution: 2.5→43.01 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2358160.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 24.2565 Å2 / ksol: 0.345166 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.5 Å2
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Refine analyze | Luzzati coordinate error free: 0.38 Å / Luzzati sigma a free: 0.39 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→43.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.275 / Rfactor Rwork: 0.22 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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