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- PDB-1sh2: Crystal Structure of Norwalk Virus Polymerase (Metal-free, Center... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1sh2 | ||||||
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Title | Crystal Structure of Norwalk Virus Polymerase (Metal-free, Centered Orthorhombic) | ||||||
![]() | RNA Polymerase | ||||||
![]() | TRANSFERASE / RNA POLYMERASE / VIRAL ENZYME / VIRAL REPLICATION | ||||||
Function / homology | ![]() ribonucleoside triphosphate phosphatase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ng, K.K. / Pendas-Franco, N. / Rojo, J. / Boga, J.A. / Machin, A. / Alonso, J.M. / Parra, F. | ||||||
![]() | ![]() Title: Crystal structure of norwalk virus polymerase reveals the carboxyl terminus in the active site cleft. Authors: Ng, K.K. / Pendas-Franco, N. / Rojo, J. / Boga, J.A. / Machin, A. / Alonso, J.M. / Parra, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111.6 KB | Display | ![]() |
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PDB format | ![]() | 86.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.8 KB | Display | ![]() |
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Full document | ![]() | 438.9 KB | Display | |
Data in XML | ![]() | 20.4 KB | Display | |
Data in CIF | ![]() | 28.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1sh0C ![]() 1sh3C ![]() 1khvS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 56813.551 Da / Num. of mol.: 1 / Fragment: C-terminus Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 8000, ammonium sulfate, Tris-Cl, glycerol, CHAPS, 2-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 2003 / Details: Mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40 Å / Num. all: 27003 / Num. obs: 27003 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.3→2.37 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2054 / Rsym value: 0.402 / % possible all: 91.3 |
Reflection | *PLUS Num. measured all: 215719 |
Reflection shell | *PLUS % possible obs: 91.3 % / Num. unique obs: 2054 / Num. measured obs: 7221 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1KHV Resolution: 2.3→36.04 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.89 / SU B: 9.887 / SU ML: 0.234 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.357 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: TLS refinement was performed for each of three domains
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.817 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→36.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 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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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.293 / Rfactor Rwork: 0.226 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.344 / Rfactor Rwork: 0.291 |