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Yorodumi- PDB-1vp3: VACCINIA VIRUS PROTEIN VP39 IN COMPLEX WITH S-ADENOSYLHOMOCYSTEINE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vp3 | ||||||
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Title | 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 / mRNA (nucleoside-2'-O-)-methyltransferase activity / RNA binding Similarity search - Function | ||||||
Biological species | Vaccinia virus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 1vp3.cif.gz | 77.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vp3.ent.gz | 56.3 KB | Display | PDB format |
PDBx/mmJSON format | 1vp3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/1vp3 ftp://data.pdbj.org/pub/pdb/validation_reports/vp/1vp3 | HTTPS FTP |
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-Related structure data
Related structure data | 1p39C 1v39C 1vp9C 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: 40156.227 Da / Num. of mol.: 1 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: 2.51 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||
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Crystal grow | pH: 4.5 / Details: pH 4.5 | ||||||||||||||||||||||||
Crystal grow | *PLUS 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: Apr 12, 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: 1.9→15 Å / Num. obs: 24966 / % possible obs: 79 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 1 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 2.2 / % possible all: 27 |
Reflection shell | *PLUS % possible obs: 27 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VPT Resolution: 1.9→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: 26.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |