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Yorodumi- PDB-4m5r: High-resolution influenza 2009 H1N1 endonuclease bound to 4-(1H-I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m5r | ||||||
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Title | High-resolution influenza 2009 H1N1 endonuclease bound to 4-(1H-IMIDAZOL-1-YL)PHENOL | ||||||
Components | Polymerase PA | ||||||
Keywords | RNA BINDING PROTEIN/INHIBITOR / CAP-SNATCHING / RNA BINDING PROTEIN-INHIBITOR complex | ||||||
Function / homology | : / 4-(1H-IMIDAZOL-1-YL)PHENOL / : Function and homology information | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Bauman, J.D. / Patel, D. / Das, K. / Arnold, E. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2013 Title: Crystallographic fragment screening and structure-based optimization yields a new class of influenza endonuclease inhibitors. Authors: Bauman, J.D. / Patel, D. / Baker, S.F. / Vijayan, R.S. / Xiang, A. / Parhi, A.K. / Martinez-Sobrido, L. / Lavoie, E.J. / Das, K. / Arnold, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m5r.cif.gz | 143.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m5r.ent.gz | 114.3 KB | Display | PDB format |
PDBx/mmJSON format | 4m5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4m5r_validation.pdf.gz | 467.4 KB | Display | wwPDB validaton report |
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Full document | 4m5r_full_validation.pdf.gz | 469 KB | Display | |
Data in XML | 4m5r_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 4m5r_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/4m5r ftp://data.pdbj.org/pub/pdb/validation_reports/m5/4m5r | HTTPS FTP |
-Related structure data
Related structure data | 4ln7C 4m4qC 4m5oC 4m5qC 4m5vC 4mk1C 4mk2C 4mk5C C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28505.270 Da / Num. of mol.: 1 / Fragment: unp residues 1-204 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Lima/WRAIR1695P/2009(H1N1)) Gene: PA / Plasmid: PCDF-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: F0TRT1 |
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-Non-polymers , 5 types, 233 molecules
#2: Chemical | ChemComp-MN / #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-EDO / | #6: Water | ChemComp-HOH / | |
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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: 2.61 Å3/Da / Density % sol: 52.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 200 MM MES, 27% PEG8K, 200 MM AMMONIUM SULFATE, 1 MM MANGANESE CHLORIDE, 10 MM MAGNESIUM ACETATE, 10 MM TAURINE, AND 50 MM SODIUM FLUORIDE, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.917 / Wavelength: 0.917 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 2, 2010 |
Radiation | Monochromator: HORIZONTAL BENT SI(111), ASYMMETRICALLY CUT WITH WATER COOLED CU BLOCK Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.917 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 65059 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 1.4→1.43 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 1.66 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→31.943 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 22.77 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→31.943 Å
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Refine LS restraints |
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LS refinement shell |
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