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- PDB-1bky: VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M1CYT AND S-ADENOS... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1bky | ||||||
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Title | VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M1CYT AND S-ADENOSYLHOMOCYSTEINE | ||||||
![]() | VP39 | ||||||
![]() | MRNA PROCESSING / METHYLATED CYTOSINE / METHYLTRANSFERASE / RNA CAP ANALOG / POLY(A) POLYMERASE / VACCINIA / TRANSCRIPTION / COMPLEX (TRANSFERASE-RNA CAP ANALOG) | ||||||
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 | ![]() | ||||||
![]() | Hu, G. / Hodel, A.E. / Gershon, P.D. / Quiocho, F.A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90 KB | Display | ![]() |
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PDB format | ![]() | 68.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 712.8 KB | Display | ![]() |
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Full document | ![]() | 718.4 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 20.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1b42C ![]() 1eamC ![]() 1eqaC ![]() 3magC ![]() 3mctC ![]() 4dcgC 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
#1: Protein | Mass: 35921.438 Da / Num. of mol.: 1 / Mutation: C-TERMINAL DELETION OF 26 RESIDUES 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: Chemical | ChemComp-1MC / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() |
Detector | Type: SIEMENS / Detector: CCD / Date: Oct 22, 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: 2→20 Å / Num. obs: 30509 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rsym value: 0.084 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 8.9 / Rsym value: 0.23 / % possible all: 99.7 |
Reflection | *PLUS Highest resolution: 1.86 Å / % possible obs: 90.7 % / Rmerge(I) obs: 0.088 |
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Processing
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Refinement | Method to determine structure: OTHER / Resolution: 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→8 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.265 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |