+Open data
-Basic information
Entry | Database: PDB / ID: 4m5q | ||||||
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Title | High-resolution apo influenza 2009 H1N1 endonuclease structure | ||||||
Components | Polymerase PA | ||||||
Keywords | RNA BINDING PROTEIN / CAP-SNATCHING | ||||||
Function / homology | : / : Function and homology information | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.534 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 | 4m5q.cif.gz | 139.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m5q.ent.gz | 111.8 KB | Display | PDB format |
PDBx/mmJSON format | 4m5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4m5q_validation.pdf.gz | 440.7 KB | Display | wwPDB validaton report |
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Full document | 4m5q_full_validation.pdf.gz | 442 KB | Display | |
Data in XML | 4m5q_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 4m5q_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/4m5q ftp://data.pdbj.org/pub/pdb/validation_reports/m5/4m5q | HTTPS FTP |
-Related structure data
Related structure data | 4ln7C 4m4qC 4m5oC 4m5rC 4m5vC 4mk1C 4mk2C 4mk5C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#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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#2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7 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 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 / Wavelength: 1.1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2012 |
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: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→50.75 Å / Num. obs: 250493 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.53→1.62 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 3.2 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.534→46.9 Å / SU ML: 0.1 / σ(F): 1.34 / Phase error: 20.76 / 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: 1.534→46.9 Å
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Refine LS restraints |
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LS refinement shell |
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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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