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Yorodumi- PDB-1vp9: DC26 MUTANT OF VACCINIA VIRUS PROTEIN VP39 IN COMPLEX WITH S-ADEN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vp9 | |||||||||
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Title | DC26 MUTANT OF VACCINIA VIRUS PROTEIN VP39 IN COMPLEX WITH S-ADENOSYLHOMOCYSTEINE | |||||||||
Components | VP39 | |||||||||
Keywords | METHYLTRANSFERASE / RNA CAP / POLY(A) POLYMERASE / VACCINIA / MRNA PROCESSING / TRANSCRIPTION | |||||||||
Function / homology | Function and homology information regulation of mRNA 3'-end processing / 7-methylguanosine mRNA capping / translation elongation factor activity / virion component / methyltransferase cap1 / methylation / mRNA (nucleoside-2'-O-)-methyltransferase activity / RNA binding Similarity search - Function | |||||||||
Biological species | Vaccinia virus | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Hodel, A.E. / Gershon, P.D. / Quiocho, F.A. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1997 Title: Specific protein recognition of an mRNA cap through its alkylated base. Authors: Hodel, A.E. / Gershon, P.D. / Shi, X. / Wang, S.M. / Quiocho, F.A. #1: Journal: Cell(Cambridge,Mass.) / Year: 1996 Title: The 1.85 A Structure of Vaccinia Protein Vp39: A Bifunctional Enzyme that Participates in the Modification of Both Mrna Ends Authors: Hodel, A.E. / Gershon, P.D. / Shi, X. / Quiocho, F.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vp9.cif.gz | 78.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vp9.ent.gz | 57.1 KB | Display | PDB format |
PDBx/mmJSON format | 1vp9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vp9_validation.pdf.gz | 704 KB | Display | wwPDB validaton report |
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Full document | 1vp9_full_validation.pdf.gz | 709.9 KB | Display | |
Data in XML | 1vp9_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 1vp9_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/1vp9 ftp://data.pdbj.org/pub/pdb/validation_reports/vp/1vp9 | HTTPS FTP |
-Related structure data
Related structure data | 1p39C 1v39C 1vp3C 2vp3C 1vptS S: Starting model for refinement 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37133.703 Da / Num. of mol.: 1 / Mutation: 26 C-TERMINAL RESIDUES DELETED Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Genus: Orthopoxvirus / Strain: WR / Cell line: BL21 / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: P07617, polynucleotide adenylyltransferase |
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#2: Chemical | ChemComp-SAH / |
#3: 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: 2.71 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4.5 Details: macro-seeding, Hodel, A.E., (1996) Cell(Cambridge,Mass.), 85, 247. Method: other | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: May 30, 1996 / Details: MIRROR |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→15 Å / Num. obs: 28062 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 31 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 5 / % possible all: 96.7 |
Reflection shell | *PLUS % possible obs: 96.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VPT Resolution: 1.95→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.0001 / Isotropic thermal model: RESTRAINED / σ(F): 2
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Displacement parameters | Biso mean: 29.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→8 Å
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Refine LS restraints |
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