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Yorodumi- PDB-2gaf: Crystal Structure of the Vaccinia Polyadenylate Polymerase Hetero... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gaf | ||||||
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Title | Crystal Structure of the Vaccinia Polyadenylate Polymerase Heterodimer (apo form) | ||||||
Components |
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Keywords | TRANSFERASE / polyadenylate polymerase / pox virus / nucleotidyltransferase / heterodimer / processivity | ||||||
Function / homology | Function and homology information regulation of mRNA 3'-end processing / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / 7-methylguanosine mRNA capping / translation elongation factor activity / virion component / mRNA processing / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / RNA binding ...regulation of mRNA 3'-end processing / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / 7-methylguanosine mRNA capping / translation elongation factor activity / virion component / mRNA processing / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / RNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Vaccinia virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Moure, C.M. / Bowman, B.R. / Gershon, P.D. / Quiocho, F.A. | ||||||
Citation | Journal: Mol.Cell / Year: 2006 Title: Crystal structures of the vaccinia virus polyadenylate polymerase heterodimer: insights into ATP selectivity and processivity. Authors: Moure, C.M. / Bowman, B.R. / Gershon, P.D. / 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 | 2gaf.cif.gz | 159.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gaf.ent.gz | 130.2 KB | Display | PDB format |
PDBx/mmJSON format | 2gaf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gaf_validation.pdf.gz | 429.1 KB | Display | wwPDB validaton report |
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Full document | 2gaf_full_validation.pdf.gz | 464.3 KB | Display | |
Data in XML | 2gaf_validation.xml.gz | 32.1 KB | Display | |
Data in CIF | 2gaf_validation.cif.gz | 44.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/2gaf ftp://data.pdbj.org/pub/pdb/validation_reports/ga/2gaf | HTTPS FTP |
-Related 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: 35057.910 Da / Num. of mol.: 1 / Mutation: R140A, K142A, R143A 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, UniProt: Q1PIV4*PLUS, methyltransferase cap1 |
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#2: Protein | Mass: 54388.844 Da / Num. of mol.: 1 / Mutation: L36S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Genus: Orthopoxvirus / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta References: UniProt: P23371, polynucleotide adenylyltransferase |
#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: 2.35 Å3/Da / Density % sol: 47.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 20% PEG 4000, 0.24 M CaCl2, 5% glycerol, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 200 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9791, 0.9793 | |||||||||
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Nov 25, 2004 | |||||||||
Radiation | Monochromator: SI (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→500 Å / Num. all: 33681 / Num. obs: 33681 / % possible obs: 83.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 | |||||||||
Reflection shell | Resolution: 2.26→2.34 Å / % possible all: 68.1 |
-Processing
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Refinement | Method to determine structure: MAD / Resolution: 2.4→500 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 46.726 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.851 Å2
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Refine analyze | Luzzati coordinate error obs: 0.35 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→500 Å
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Refine LS restraints |
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Xplor file |
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