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Yorodumi- PDB-4cb4: Structure of Influenza A H5N1 PB2 cap-binding domain with bound m7GTP -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cb4 | ||||||
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Title | Structure of Influenza A H5N1 PB2 cap-binding domain with bound m7GTP | ||||||
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: 1.6 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 | 4cb4.cif.gz | 95.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cb4.ent.gz | 71.3 KB | Display | PDB format |
PDBx/mmJSON format | 4cb4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/4cb4 ftp://data.pdbj.org/pub/pdb/validation_reports/cb/4cb4 | HTTPS FTP |
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-Related structure data
Related structure data | 4cb5C 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 / Strain: A/DUCK/SHANTOU/4610/2003(H5N1) / Plasmid: PET-M11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUS RIL / References: UniProt: Q2LG68 | ||||||
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#2: Chemical | ChemComp-MGT / | ||||||
#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: 2.88 Å3/Da / Density % sol: 57.4 % / Description: NONE |
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Crystal grow | pH: 4.6 / Details: 0.1M SODIUM ACETATE PH 4.6, 2M NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 28140 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.72 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.62 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.65 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.52 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VQZ Resolution: 1.6→43.35 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.62 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.069 / 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: 17.205 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→43.35 Å
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Refine LS restraints |
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