+Open data
-Basic information
Entry | Database: PDB / ID: 7oec | |||||||||
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Title | Crystal structure of an intein from a hyperthermophile | |||||||||
Components | DNA polymerase II large subunit | |||||||||
Keywords | SPLICING / protein splicing / intein | |||||||||
Function / homology | Function and homology information exodeoxyribonuclease I / single-stranded DNA 3'-5' DNA exonuclease activity / intein-mediated protein splicing / DNA catabolic process / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / identical protein binding Similarity search - Function | |||||||||
Biological species | Pyrococcus horikoshii (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å | |||||||||
Authors | Hannes, B. / Hiltunen, M. / Iwai, H. | |||||||||
Funding support | Finland, 1items
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Citation | Journal: Microorganisms / Year: 2021 Title: Mini-Intein Structures from Extremophiles Suggest a Strategy for Finding Novel Robust Inteins. Authors: Hiltunen, M.K. / Beyer, H.M. / Iwai, H. #1: Journal: Preprints / Year: 2021 Title: Mini-Intein Structures from Extremophiles Suggest a Strategy for Finding Novel Robust Inteins Authors: Hiltunen, M.K. / Beyer, H.M. / Iwai, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7oec.cif.gz | 137.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oec.ent.gz | 90.7 KB | Display | PDB format |
PDBx/mmJSON format | 7oec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/7oec ftp://data.pdbj.org/pub/pdb/validation_reports/oe/7oec | HTTPS FTP |
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-Related structure data
Related structure data | 6rpqS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19454.188 Da / Num. of mol.: 1 / Mutation: C1A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea) Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3 Gene: polC, PH0121 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express References: UniProt: O57861, DNA-directed DNA polymerase, exodeoxyribonuclease I | ||||||||
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#2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM MES pH 6, 15 % (W/v) PEG 550 MME, 30 mM zinc sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 24, 2019 |
Radiation | Monochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→35.41 Å / Num. obs: 30560 / % possible obs: 99.87 % / Redundancy: 25.4 % / Biso Wilson estimate: 23.39 Å2 / CC1/2: 0.998 / Net I/σ(I): 16.35 |
Reflection shell | Resolution: 1.48→1.533 Å / Mean I/σ(I) obs: 4.22 / Num. unique obs: 2977 / CC1/2: 0.445 / % possible all: 99.97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6RPQ Resolution: 1.48→35.41 Å / SU ML: 0.1201 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.5066 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 29.71 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.48→35.41 Å
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Refine LS restraints |
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LS refinement shell |
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