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- PDB-4che: Crystal structure of the putative cap-binding domain of the PB2 s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4che | ||||||
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Title | Crystal structure of the putative cap-binding domain of the PB2 subunit of Thogoto virus polymerase | ||||||
![]() | POLYMERASE BASIC PROTEIN 2 | ||||||
![]() | VIRAL PROTEIN | ||||||
Function / homology | ![]() cap snatching / 7-methylguanosine mRNA capping / virion component / host cell nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guilligay, D. / Kadlec, J. / Crepin, T. / Lunardi, T. / Bouvier, D. / Kochs, G. / Ruigrok, R.W.H. / Cusack, S. | ||||||
![]() | ![]() Title: Comparative Structural and Functional Analysis of Orthomyxovirus Polymerase CAP-Snatching Domains. Authors: Guilligay, D. / Kadlec, J. / Crepin, T. / Lunardi, T. / Bouvier, D. / Kochs, G. / Ruigrok, R.W.H. / Cusack, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.7 KB | Display | ![]() |
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PDB format | ![]() | 35.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 19318.199 Da / Num. of mol.: 1 / Fragment: PUTATIVE CAP-BINDING DOMAIN, RESIDUES 323-486 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
Sequence details | EXTRA GAMA AT N-TERMINUS AFTER HIS-TAG CLEAVAGE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.4 % / Description: SELENOMETHIONINE SAD |
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Crystal grow | Temperature: 293 K / pH: 6 Details: THE PROTEIN WAS CONCENTRATED TO 9 MG/ML IN A BUFFER CONTAINING 20 MM TRIS PH 7.0, 200 MM NACL AND 5 MM BETA-MERCAPTOETHANOL. THE BEST-DIFFRACTING CRYSTALS GREW WITHIN 2 DAYS AT 20 C IN A ...Details: THE PROTEIN WAS CONCENTRATED TO 9 MG/ML IN A BUFFER CONTAINING 20 MM TRIS PH 7.0, 200 MM NACL AND 5 MM BETA-MERCAPTOETHANOL. THE BEST-DIFFRACTING CRYSTALS GREW WITHIN 2 DAYS AT 20 C IN A SOLUTION CONTAINING 100 MM BIS-TRIS PH 6.0, 100 MM MGCL2 AND 22 % PEG3350. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 20, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 21746 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.4 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 1.8→77.62 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.049 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.115 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→77.62 Å
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Refine LS restraints |
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