[English] 日本語
Yorodumi- PDB-4dcg: VACCINIA METHYLTRANSFERASE VP39 MUTANT D182A COMPLEXED WITH M7G A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dcg | ||||||
---|---|---|---|---|---|---|---|
Title | VACCINIA METHYLTRANSFERASE VP39 MUTANT D182A COMPLEXED WITH M7G AND S-ADENOSYLHOMOCYSTEINE | ||||||
Components | VP39 | ||||||
Keywords | MRNA PROCESSING / METHYLATED GUANOSINE / METHYLTRANSFERASE MUTANT D182A / RNA CAP ANALOG / POLY(A) POLYMERASE / VACCINIA / 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: 1.8 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4dcg.cif.gz | 92.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4dcg.ent.gz | 70.4 KB | Display | PDB format |
PDBx/mmJSON format | 4dcg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dcg_validation.pdf.gz | 985.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4dcg_full_validation.pdf.gz | 991.5 KB | Display | |
Data in XML | 4dcg_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 4dcg_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/4dcg ftp://data.pdbj.org/pub/pdb/validation_reports/dc/4dcg | HTTPS FTP |
-Related structure data
Related structure data | 1b42C 1bkyC 1eamC 1eqaC 3magC 3mctC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 35877.426 Da / Num. of mol.: 1 / Mutation: D182A, C-TERMINAL DELETION OF 26 RESIDUES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Genus: Orthopoxvirus / Strain: BL21 (DE3) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: P07617, polynucleotide adenylyltransferase |
---|---|
#2: Chemical | ChemComp-SAH / |
#3: Chemical | ChemComp-MG7 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 103 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: CCD / Date: Oct 28, 1997 / 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: 1.83→20 Å / Num. obs: 31782 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rsym value: 0.05 / Net I/σ(I): 24 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 10 / Rsym value: 0.2 / % possible all: 92 |
Reflection | *PLUS % possible obs: 91.8 % / Rmerge(I) obs: 0.051 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: OTHER / Resolution: 1.8→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.0001 / Cross valid method: FREE-R / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|