+Open data
-Basic information
Entry | Database: PDB / ID: 7.0E+15 | ||||||
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Title | Protein ternary complex working for DNA replication initiation | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/REPLICATION / DNA replication / DNA BINDING PROTEIN-REPLICATION COMPLEX / REPLICATION | ||||||
Function / homology | Function and homology information DNA polymerase complex / exodeoxyribonuclease I / single-stranded DNA 3'-5' DNA exonuclease activity / DNA catabolic process / DNA strand elongation involved in DNA replication / exonuclease activity / nucleic acid binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding Similarity search - Function | ||||||
Biological species | Thermococcus kodakarensis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Oyama, T. / Ishino, Y. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2022 Title: Family D DNA polymerase interacts with GINS to promote CMG-helicase in the archaeal replisome. Authors: Oki, K. / Nagata, M. / Yamagami, T. / Numata, T. / Ishino, S. / Oyama, T. / Ishino, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e15.cif.gz | 266.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e15.ent.gz | 183.5 KB | Display | PDB format |
PDBx/mmJSON format | 7e15.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/7e15 ftp://data.pdbj.org/pub/pdb/validation_reports/e1/7e15 | HTTPS FTP |
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-Related structure data
Related structure data | 5ghrS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 52910.023 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea) Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK1252 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5JGL0 #2: Protein | Mass: 9008.398 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea) Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK0536 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5JF31 #3: Protein | Mass: 7251.381 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea) Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: polB, TK1902 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q5JET1, DNA-directed DNA polymerase, exodeoxyribonuclease I #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.31 % Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.15 M DL-malic acid (pH 7.0), 20 % (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 29, 2017 / Details: two dimensional focusing mirror |
Radiation | Monochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. obs: 93014 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 31.22 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.077 / Rrim(I) all: 0.11 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.45→2.49 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 2 / Num. unique obs: 16322 / CC1/2: 0.927 / Rpim(I) all: 0.395 / Rrim(I) all: 0.56 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ghr Resolution: 2.45→47.01 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0.16 / Phase error: 30.6113 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.54 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→47.01 Å
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Refine LS restraints |
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LS refinement shell |
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