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Yorodumi- PDB-1b42: VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M1ADE AND S-ADENOS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b42 | ||||||
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Title | VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M1ADE AND S-ADENOSYLHOMOCYSTEINE | ||||||
Components | VP39 | ||||||
Keywords | METHYLTRANSFERASE / METHYLATED ADENINE / RNA CAP ANALOG / POLY (A) POLYMERASE / VACCINIA / MRNA PROCESSING / TRANSCRIPTION / COMPLEX (TRANSFERASE-RNA CAP ANALOG) | ||||||
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 / OTHER / Resolution: 2.2 Å | ||||||
Authors | Hu, G. / Hodel, A.E. / Gershon, P.D. / Quiocho, F.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 Title: mRNA cap recognition: dominant role of enhanced stacking interactions between methylated bases and protein aromatic side chains. Authors: Hu, G. / Gershon, P.D. / Hodel, A.E. / 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 | 1b42.cif.gz | 93.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b42.ent.gz | 71.8 KB | Display | PDB format |
PDBx/mmJSON format | 1b42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b42_validation.pdf.gz | 711.9 KB | Display | wwPDB validaton report |
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Full document | 1b42_full_validation.pdf.gz | 721.1 KB | Display | |
Data in XML | 1b42_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 1b42_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/1b42 ftp://data.pdbj.org/pub/pdb/validation_reports/b4/1b42 | HTTPS FTP |
-Related structure data
Related structure data | 1bkyC 1eamC 1eqaC 3magC 3mctC 4dcgC 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
#1: Protein | Mass: 34819.293 Da / Num. of mol.: 1 / Mutation: C-TERMINAL DELETION OF 26 RESIDUES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Genus: Orthopoxvirus / 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: Chemical | ChemComp-M1A / |
#4: 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: 2.77 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4.5 / Method: otherDetails: used macroseeding, Hodel, A.E., (1996) Cell, 85, 247. | ||||||||||||||||||||||||
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: SIEMENS / Detector: CCD / Date: Sep 10, 1998 / Details: GOBEL 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: 2.2→99 Å / Num. obs: 15892 / % possible obs: 77.7 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rsym value: 0.055 |
Reflection shell | Resolution: 2.2→2.28 Å / Rsym value: 0.133 / % possible all: 44 |
Reflection | *PLUS Rmerge(I) obs: 0.055 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.2→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.0001 / Cross valid method: FREE-R / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Xplor file |
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