[English] 日本語
Yorodumi- PDB-3kc6: Crystal structure of the large c-terminal domain of polymerase ba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kc6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the large c-terminal domain of polymerase basic protein 2 from influenza virus a/viet nam/1203/2004 (h5n1) | ||||||
Components | Polymerase PB2 | ||||||
Keywords | VIRAL PROTEIN / Bird flu / structural genomics / NIAID / mRNA capping / mRNA processing / Seattle Structural Genomics Center for Infectious Disease / SSGCID | ||||||
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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / RNA binding Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: Plos Pathog. / Year: 2010 Title: Biological and structural characterization of a host-adapting amino acid in influenza virus. Authors: Yamada, S. / Hatta, M. / Staker, B.L. / Watanabe, S. / Imai, M. / Shinya, K. / Sakai-Tagawa, Y. / Ito, M. / Ozawa, M. / Watanabe, T. / Sakabe, S. / Li, C. / Kim, J.H. / Myler, P.J. / Phan, I. ...Authors: Yamada, S. / Hatta, M. / Staker, B.L. / Watanabe, S. / Imai, M. / Shinya, K. / Sakai-Tagawa, Y. / Ito, M. / Ozawa, M. / Watanabe, T. / Sakabe, S. / Li, C. / Kim, J.H. / Myler, P.J. / Phan, I. / Raymond, A. / Smith, E. / Stacy, R. / Nidom, C.A. / Lank, S.M. / Wiseman, R.W. / Bimber, B.N. / O'Connor, D.H. / Neumann, G. / Stewart, L.J. / Kawaoka, Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3kc6.cif.gz | 54.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3kc6.ent.gz | 37.9 KB | Display | PDB format |
PDBx/mmJSON format | 3kc6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kc6_validation.pdf.gz | 437.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3kc6_full_validation.pdf.gz | 438.6 KB | Display | |
Data in XML | 3kc6_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 3kc6_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/3kc6 ftp://data.pdbj.org/pub/pdb/validation_reports/kc/3kc6 | HTTPS FTP |
-Related structure data
Related structure data | 3khwC 3l56C 3cw4S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | UNKNOWN |
-Components
#1: Protein | Mass: 22765.184 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Viet Nam/1203/2004(H5N1)) Strain: A/VIET NAM/1203/2004 (H5N1) / Gene: PB2 / Plasmid: PET28-SMT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6DNN3 | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.79 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.5 Details: 5% SBOG, 100MM CAPS PH 10.5, 1.2 M SODIUM PHOSPHATE, 0.2 M LITHIUM PHOSPHATE, 0.8 M POTASSIUM PHOSPHATE. PROTEIN CONCENTRATION 8.25 MG/ML, VAPOR DIFFUSIONI, SITTING DROP, TEMPERATURE 293K, ...Details: 5% SBOG, 100MM CAPS PH 10.5, 1.2 M SODIUM PHOSPHATE, 0.2 M LITHIUM PHOSPHATE, 0.8 M POTASSIUM PHOSPHATE. PROTEIN CONCENTRATION 8.25 MG/ML, VAPOR DIFFUSIONI, SITTING DROP, TEMPERATURE 293K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 31, 2009 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 13728 / % possible obs: 98.7 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 4 % / Rmerge(I) obs: 0.328 / % possible all: 88.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CW4 Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.239 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.38 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.05→2.1 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|