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- PDB-3hw5: crystal structure of avian influenza virus PA_N in complex with AMP -
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Open data
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Basic information
Entry | Database: PDB / ID: 3hw5 | ||||||
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Title | crystal structure of avian influenza virus PA_N in complex with AMP | ||||||
![]() | Polymerase acidic protein | ||||||
![]() | HYDROLASE / avian influenza virus / PA_N / AMP / Phosphoprotein | ||||||
Function / homology | ![]() cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhao, C. / Lou, Z. / Guo, Y. / Ma, M. / Chen, Y. / Liang, S. / Rao, Z. | ||||||
![]() | ![]() Title: Nucleoside monophosphate complex structures of the endonuclease domain from the influenza virus polymerase PA subunit reveal the substrate binding site inside the catalytic center Authors: Zhao, C. / Lou, Z. / Guo, Y. / Ma, M. / Chen, Y. / Liang, S. / Zhang, L. / Chen, S. / Li, X. / Liu, Y. / Bartlam, M. / Rao, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 178.3 KB | Display | ![]() |
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PDB format | ![]() | 137.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 896.7 KB | Display | ![]() |
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Full document | ![]() | 927.4 KB | Display | |
Data in XML | ![]() | 39.5 KB | Display | |
Data in CIF | ![]() | 55.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hw3C ![]() 3hw4C ![]() 3hw6C ![]() 3ebjS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30324.307 Da / Num. of mol.: 4 / Fragment: residues in UNP 1- 256 / Mutation: V201I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: PA / Plasmid: pGEX-6p-1 / Production host: ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-AMP / | #4: Water | ChemComp-HOH / | Sequence details | THE AUTHORS BELIEVE THAT ILE 201 IS CORRECT AND IT IS NATURAL MUTANT. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 42.4 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 17.5% PEG3350(w/v), 100mM MgAc, 100mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 28, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 63099 / Num. obs: 65112 / % possible obs: 96 % / Observed criterion σ(F): 0 / Rmerge(I) obs: 0.054 |
Reflection shell | Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.128 / Num. unique all: 7817 / % possible all: 96 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3EBJ Resolution: 1.81→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.261 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 29.176 Å2
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Refinement step | Cycle: LAST / Resolution: 1.81→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.805→1.852 Å / Total num. of bins used: 20
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