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Yorodumi- PDB-4iuj: Structure of Polymerase acid protein (PA) from Influenzavirus A I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4iuj | ||||||
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Title | Structure of Polymerase acid protein (PA) from Influenzavirus A Influenza A virus A, WILSON-SMITH/1933 (H1N1) | ||||||
Components | Polymerase acidic protein | ||||||
Keywords | TRANSCRIPTION / SSGCID / Influenza / H1N1 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information RNA polymerase activity / negative regulation of viral transcription / negative stranded viral RNA replication / negative regulation of viral genome replication / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / protein import into nucleus / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds ...RNA polymerase activity / negative regulation of viral transcription / negative stranded viral RNA replication / negative regulation of viral genome replication / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / protein import into nucleus / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / viral translational frameshifting / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: Sci Rep / Year: 2014 Title: Structural analysis of H1N1 and H7N9 influenza A virus PA in the absence of PB1. Authors: Moen, S.O. / Abendroth, J. / Fairman, J.W. / Baydo, R.O. / Bullen, J. / Kirkwood, J.L. / Barnes, S.R. / Raymond, A.C. / Begley, D.W. / Henkel, G. / McCormack, K. / Tam, V.C. / Phan, I. / ...Authors: Moen, S.O. / Abendroth, J. / Fairman, J.W. / Baydo, R.O. / Bullen, J. / Kirkwood, J.L. / Barnes, S.R. / Raymond, A.C. / Begley, D.W. / Henkel, G. / McCormack, K. / Tam, V.C. / Phan, I. / Staker, B.L. / Stacy, R. / Myler, P.J. / Lorimer, D. / Edwards, T.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4iuj.cif.gz | 181.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iuj.ent.gz | 142.8 KB | Display | PDB format |
PDBx/mmJSON format | 4iuj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4iuj_validation.pdf.gz | 420.5 KB | Display | wwPDB validaton report |
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Full document | 4iuj_full_validation.pdf.gz | 423.9 KB | Display | |
Data in XML | 4iuj_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 4iuj_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/4iuj ftp://data.pdbj.org/pub/pdb/validation_reports/iu/4iuj | HTTPS FTP |
-Related structure data
Related structure data | 4p9aC 2znlS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 53096.723 Da / Num. of mol.: 1 / Fragment: UNP residues 254-713 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Wilson-Smith/1933(H1N1) / Gene: PA / Plasmid: InvaN.07057.a.D15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P15659 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 52 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Molecular Dimensions Morpheus screen g50: 10% PEG 8000, 20% ethylene glycol; 20mM of each Na-formate, Ammonium-acetate, Na3-citrate, NaK D/L tartrate, Na-oxamate; 100mM MOPS/HEPES pH 7.5; ...Details: Molecular Dimensions Morpheus screen g50: 10% PEG 8000, 20% ethylene glycol; 20mM of each Na-formate, Ammonium-acetate, Na3-citrate, NaK D/L tartrate, Na-oxamate; 100mM MOPS/HEPES pH 7.5; INVAN.07057.A.D15.PD909136 AT 20.45MG/ML, direct cryo, vapor diffusion, sitting drop, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. all: 45568 / Num. obs: 45117 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Biso Wilson estimate: 35.36 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 19.09 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2znl Resolution: 1.9→47.6 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.2071 / WRfactor Rwork: 0.1795 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.898 / SU B: 4.784 / SU ML: 0.073 / SU R Cruickshank DPI: 0.1169 / SU Rfree: 0.1113 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 92.82 Å2 / Biso mean: 37.196 Å2 / Biso min: 18.74 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→47.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 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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