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Yorodumi- PDB-4cb7: Structure of Influenza A H5N1 PB2 cap-binding domain with bound c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cb7 | ||||||
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Title | Structure of Influenza A H5N1 PB2 cap-binding domain with bound cap analogue (compound 8e) | ||||||
Components | POLYMERASE BASIC SUBUNIT 2 | ||||||
Keywords | TRANSCRIPTION / CAP-BINDING INHIBITORS | ||||||
Function / homology | Function and homology information cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / virion component / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding Similarity search - Function | ||||||
Biological species | INFLUENZA A VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Pautus, S. / Sehr, P. / Lewis, J. / Fortune, A. / Wolkerstorfer, A. / Szolar, O. / Gulligay, D. / Lunardi, T. / Decout, J.L. / Cusack, S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: New 7-Methyl-Guanosine Derivatives Targeting the Influenza Polymerase Pb2 CAP-Binding Domain Authors: Pautus, S. / Sehr, P. / Lewis, J. / Fortune, A. / Wolkerstorfer, A. / Szolar, O. / Gulligay, D. / Lunardi, T. / Decout, J.L. / Cusack, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cb7.cif.gz | 79.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cb7.ent.gz | 58.8 KB | Display | PDB format |
PDBx/mmJSON format | 4cb7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cb7_validation.pdf.gz | 730.2 KB | Display | wwPDB validaton report |
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Full document | 4cb7_full_validation.pdf.gz | 731.3 KB | Display | |
Data in XML | 4cb7_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 4cb7_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/4cb7 ftp://data.pdbj.org/pub/pdb/validation_reports/cb/4cb7 | HTTPS FTP |
-Related structure data
Related structure data | 4cb4C 4cb5C 4cb6C 2vqzS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18248.199 Da / Num. of mol.: 2 / Fragment: CAP-BINDING DOMAIN, RESIDUES 318-483 / Mutation: YES Source method: isolated from a genetically manipulated source Details: LOOP DELETION VARIANT / Source: (gene. exp.) INFLUENZA A VIRUS / Strain: A/DUCK/SHANTOU/4610/2003(H5N1) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUS RIL / References: UniProt: Q2LG68 #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-41G / | #4: Water | ChemComp-HOH / | Sequence details | EXTRA N-TERMINAL GLYCINE AFTER HIS-TAG CLEAVAGE LOOP DELETION VARIANT 420-FVNRANQRLN | |
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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: 2.07 Å3/Da / Density % sol: 40.7 % / Description: NONE |
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Crystal grow | pH: 6.3 / Details: 0.2M AMMONIUM NITRATE, PH 6.3, 20 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9749 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 30, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9749 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 25819 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 3.29 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.85→1.94 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.8 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VQZ Resolution: 1.85→36.96 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.968 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.134 / 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: 25.504 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→36.96 Å
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Refine LS restraints |
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