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Yorodumi- PDB-1t7p: T7 DNA POLYMERASE COMPLEXED TO DNA PRIMER/TEMPLATE,A NUCLEOSIDE T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t7p | ||||||
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Title | T7 DNA POLYMERASE COMPLEXED TO DNA PRIMER/TEMPLATE,A NUCLEOSIDE TRIPHOSPHATE, AND ITS PROCESSIVITY FACTOR THIOREDOXIN | ||||||
Components |
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Keywords | TRANSFERASE/DNA / T7 DNA POLYMERASE / DNA REPLICATION / NUCLEOTIDYL TRANSFERASE / THIOREDOXIN / PROCESSIVITY FACTOR / COMPLEX (HYDROLASE-ELECTRON TRANSPORT-DNA) / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information DNA synthesis involved in DNA replication / DNA exonuclease activity / viral DNA genome replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA polymerase processivity factor activity / protein-disulfide reductase activity / 3'-5' exonuclease activity / cell redox homeostasis / DNA-templated DNA replication / DNA-directed DNA polymerase ...DNA synthesis involved in DNA replication / DNA exonuclease activity / viral DNA genome replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA polymerase processivity factor activity / protein-disulfide reductase activity / 3'-5' exonuclease activity / cell redox homeostasis / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Enterobacteria phage T7 (virus) Escherichia coli O157:H7 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Doublie, S. / Tabor, S. / Long, A.M. / Richardson, C.C. / Ellenberger, T. | ||||||
Citation | Journal: Nature / Year: 1998 Title: Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution. Authors: Doublie, S. / Tabor, S. / Long, A.M. / Richardson, C.C. / Ellenberger, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t7p.cif.gz | 195.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t7p.ent.gz | 147.2 KB | Display | PDB format |
PDBx/mmJSON format | 1t7p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t7/1t7p ftp://data.pdbj.org/pub/pdb/validation_reports/t7/1t7p | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA chain , 2 types, 2 molecules PT
#1: DNA chain | Mass: 3327.200 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3943.559 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 2 types, 2 molecules AB
#3: Protein | Mass: 79089.789 Da / Num. of mol.: 1 / Mutation: DEL(118-123) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T7 (virus) / Genus: T7-like viruses / Production host: Escherichia coli (E. coli) References: UniProt: P00581, DNA-directed DNA polymerase, Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters |
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#4: Protein | Mass: 11687.388 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: trxA, Z5291, ECs4714 / References: UniProt: P0AA27, UniProt: P0AA25*PLUS |
-Non-polymers , 3 types, 507 molecules
#5: Chemical | ChemComp-DG3 / | ||
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#6: Chemical | #7: 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: 3.05 Å3/Da / Density % sol: 59.7 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: unknown / Details: used to seeding | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. obs: 162012 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rsym value: 0.054 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 6.5 / Rsym value: 0.15 / % possible all: 86.7 |
Reflection | *PLUS Num. obs: 60190 / Num. measured all: 162012 / Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS % possible obs: 86.7 % / Rmerge(I) obs: 0.151 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 23.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.24 / Rfactor Rwork: 0.24 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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