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- PDB-1vp3: VACCINIA VIRUS PROTEIN VP39 IN COMPLEX WITH S-ADENOSYLHOMOCYSTEINE -
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Open data
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Basic information
Entry | Database: PDB / ID: 1vp3 | ||||||
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Title | VACCINIA VIRUS PROTEIN VP39 IN COMPLEX WITH S-ADENOSYLHOMOCYSTEINE | ||||||
![]() | VP39 | ||||||
![]() | METHYLTRANSFERASE / RNA CAP / POLY(A) POLYMERASE / VACCINIA / MRNA PROCESSING / TRANSCRIPTION | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hodel, A.E. / Gershon, P.D. / Quiocho, F.A. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.8 KB | Display | ![]() |
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PDB format | ![]() | 56.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 716.1 KB | Display | ![]() |
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Full document | ![]() | 721.3 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 21.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1p39C ![]() 1v39C ![]() 1vp9C ![]() 2vp3C ![]() 1vptS S: Starting model for refinement C: citing same article ( |
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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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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.) ![]() ![]() ![]() ![]() References: UniProt: P07617, polynucleotide adenylyltransferase |
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#2: Chemical | ChemComp-SAH / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() |
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 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() 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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |