+Open data
-Basic information
Entry | Database: PDB / ID: 1noy | ||||||
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Title | DNA POLYMERASE (E.C.2.7.7.7)/DNA COMPLEX | ||||||
Components |
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Keywords | TRANSFERASE/DNA / EXONUCLEASE / DNA-BINDING / COMPLEX (NUCLEOTIDYLTRANSFERASE-DNA) / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / 3'-5'-DNA exonuclease activity / DNA replication proofreading / SOS response / 3'-5' exonuclease activity / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity ...bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / 3'-5'-DNA exonuclease activity / DNA replication proofreading / SOS response / 3'-5' exonuclease activity / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Wang, J. / Yu, P. / Lin, T.C. / Konigsberg, W.H. / Steitz, T.A. | ||||||
Citation | Journal: Biochemistry / Year: 1996 Title: Crystal structures of an NH2-terminal fragment of T4 DNA polymerase and its complexes with single-stranded DNA and with divalent metal ions. Authors: Wang, J. / Yu, P. / Lin, T.C. / Konigsberg, W.H. / Steitz, T.A. #1: Journal: J.Biol.Chem. / Year: 1994 Title: Isolation, Characterization, and Kinetic Properties of Truncated Forms of T4 DNA Polymerase that Exhibit 3'-5' Exonuclease Activity Authors: Lin, T.C. / Karam, G. / Konigsberg, W.H. #2: Journal: J.Biol.Chem. / Year: 1988 Title: Primary Structure of T4 DNA Polymerase. Evolutionary Relatedness to Eucaryotic and Other Procaryotic DNA Polymerases Authors: Spicer, E.K. / Rush, J. / Fung, C. / Reha-Krantz, L.J. / Karam, J.D. / Konigsberg, W.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1noy.cif.gz | 156.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1noy.ent.gz | 128.8 KB | Display | PDB format |
PDBx/mmJSON format | 1noy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1noy_validation.pdf.gz | 413.5 KB | Display | wwPDB validaton report |
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Full document | 1noy_full_validation.pdf.gz | 438.9 KB | Display | |
Data in XML | 1noy_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 1noy_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/1noy ftp://data.pdbj.org/pub/pdb/validation_reports/no/1noy | 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: DNA chain | Mass: 867.621 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||||
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#2: Protein | Mass: 45315.727 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Production host: Escherichia coli (E. coli) / References: UniProt: P04415 #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-MN / | #5: 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: 2.41 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||
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Crystal | *PLUS Density % sol: 50 % | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Oct 7, 1993 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | % possible obs: 100 % |
Reflection | *PLUS Highest resolution: 2.2 Å / Rmerge(I) obs: 0.096 |
-Processing
Software |
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Refinement | Resolution: 2.2→6 Å / σ(F): 2 Details: THIS STRUCTURE WAS DETERMINED AT ROOM TEMPERATURE (298K). THE DIVALENT AND P(DT)3 WERE DETERMINED FROM TWO SEPARATE EXPERIMENTS AT LOWER RESOLUTIONS, CONCATENATED TOGETHER IN THIS ENTRY. ASP ...Details: THIS STRUCTURE WAS DETERMINED AT ROOM TEMPERATURE (298K). THE DIVALENT AND P(DT)3 WERE DETERMINED FROM TWO SEPARATE EXPERIMENTS AT LOWER RESOLUTIONS, CONCATENATED TOGETHER IN THIS ENTRY. ASP 1, GLU 2, ILE 211 AND FOUR OTHER RESIDUES WERE IDENTIFIED FROM ELECTRON DENSITY MAPS, BUT THE AUTHORS HAVE NOT DONE DNA SEQUENCING TO CONFIRM POSSIBLE SPONTANEOUSLY MUTATIONS. ILE 211 WAS REPLACED BY THR 211 IN THIS ENTRY WITHOUT ADDITIONAL REFINEMENT BY REMOVING ATOM CD1.
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Refinement step | Cycle: LAST / Resolution: 2.2→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 6 Å / σ(F): 2 / Rfactor obs: 0.222 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 39.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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