+Open data
-Basic information
Entry | Database: PDB / ID: 1n1h | ||||||
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Title | Initiation complex of polymerase lambda3 from reovirus | ||||||
Components |
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Keywords | TRANSFERASE/RNA / polymerase / initiation complex / right hand configuration / 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: 2.8 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 | 1n1h.cif.gz | 273.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n1h.ent.gz | 212.9 KB | Display | PDB format |
PDBx/mmJSON format | 1n1h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n1h_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1n1h_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1n1h_validation.xml.gz | 51.6 KB | Display | |
Data in CIF | 1n1h_validation.cif.gz | 71.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/1n1h ftp://data.pdbj.org/pub/pdb/validation_reports/n1/1n1h | HTTPS FTP |
-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 / Protein , 2 types, 2 molecules BA
#1: RNA chain | Mass: 1876.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: AUUAGC, RNA oligo ordered from Dharmacon |
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#2: 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 |
-Non-polymers , 6 types, 189 molecules
#3: Chemical | #4: Chemical | ChemComp-G7M / | #5: Chemical | ChemComp-GDP / | #6: Chemical | ChemComp-CH1 / | #7: Chemical | ChemComp-GH3 / | #8: 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: 2.6 Å3/Da / Density % sol: 52.72 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: APS / Beamline: 19-ID / Wavelength: 1.03 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Nov 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 30558 / Num. obs: 30558 / % possible obs: 79.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2846 / % possible all: 75.6 |
Reflection | *PLUS Lowest resolution: 30 Å / Redundancy: 2-3 / Rmerge(I) obs: 0.12 |
Reflection shell | *PLUS % possible obs: 75.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: lambda3 native structure Resolution: 2.8→29.71 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 16.4353 Å2 / ksol: 0.365407 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.8 Å2
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Refine analyze | Luzzati coordinate error free: 0.42 Å / Luzzati sigma a free: 0.43 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→29.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.9 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.193 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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