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Yorodumi- PDB-4cb5: Structure of Influenza A H5N1 PB2 cap-binding domain with bound c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cb5 | ||||||
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Title | Structure of Influenza A H5N1 PB2 cap-binding domain with bound cap analogue (compound 8f) | ||||||
Components | POLYMERASE BASIC SUBUNIT 2 | ||||||
Keywords | TRANSFERASE / 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: 1.5 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 | 4cb5.cif.gz | 83.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cb5.ent.gz | 61.3 KB | Display | PDB format |
PDBx/mmJSON format | 4cb5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cb5_validation.pdf.gz | 742.6 KB | Display | wwPDB validaton report |
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Full document | 4cb5_full_validation.pdf.gz | 743.7 KB | Display | |
Data in XML | 4cb5_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 4cb5_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/4cb5 ftp://data.pdbj.org/pub/pdb/validation_reports/cb/4cb5 | HTTPS FTP |
-Related structure data
Related structure data | 4cb4C 4cb6C 4cb7C 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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Unit cell |
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-Components
#1: Protein | Mass: 18887.951 Da / Num. of mol.: 1 / Fragment: CAP-BINDING DOMAIN, RESIDUES 318-483 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/duck/Shantou/4610/2003(H5N1)) Plasmid: PET-M11 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): CODONPLUS RIL / References: UniProt: Q2LG68 | ||||||
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#2: Chemical | ChemComp-93G / | ||||||
#3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | CHLORIDE ION (CL): FROM CRYSTALLIS | Sequence details | EXTRA N-TERMINAL GLYCINE AFTER HIS-TAG CLEAVAGE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.8 % / Description: NONE |
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Crystal grow | pH: 4.3 / Details: 1M SODIUM ACETATE PH 4.3, 2.4M NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 18, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 33681 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.68 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.5→1.56 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.9 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VQZ Resolution: 1.5→43.48 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.334 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.051 / 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: 16.541 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→43.48 Å
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Refine LS restraints |
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