+Open data
-Basic information
Entry | Database: PDB / ID: 7z82 | |||||||||
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Title | REP-related Chom18 variant with double AG mismatch | |||||||||
Components | Chom18-AG DNA | |||||||||
Keywords | DNA / Mismatch / Non-canonical / Base pair / Double helix | |||||||||
Function / homology | STRONTIUM ION / DNA / DNA (> 10) Function and homology information | |||||||||
Biological species | Cardiobacterium hominis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | |||||||||
Authors | Svoboda, J. / Kolenko, P. / Berdar, D. / Schneider, B. | |||||||||
Funding support | Czech Republic, 2items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2023 Title: Conformation-based refinement of 18-mer DNA structures. Authors: Svoboda, J. / Berdar, D. / Kolenko, P. / Cerny, J. / Novakova, Z. / Pavlicek, J. / Schneider, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z82.cif.gz | 23.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z82.ent.gz | 11.8 KB | Display | PDB format |
PDBx/mmJSON format | 7z82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/7z82 ftp://data.pdbj.org/pub/pdb/validation_reports/z8/7z82 | HTTPS FTP |
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-Related structure data
Related structure data | 7z7kC 7z7lC 7z7mC 7z7uC 7z7wC 7z7yC 7z7zC 7z81C 6rosS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 5543.567 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Cardiobacterium hominis (bacteria) |
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#2: Chemical | ChemComp-SR / |
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: 2.88 Å3/Da / Density % sol: 57.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Natrix crystallization screen (Hampton Research) precipitant 18-22% (+/-)-2-Methyl-2,4-pentanediol buffer 0.04 M Sodium cacodylate trihydrate salt 0.04 M Magnezium chloride hexahydrate 0.08 ...Details: Natrix crystallization screen (Hampton Research) precipitant 18-22% (+/-)-2-Methyl-2,4-pentanediol buffer 0.04 M Sodium cacodylate trihydrate salt 0.04 M Magnezium chloride hexahydrate 0.08 M Strontium chloride hexahydrate additive 0.012 M spermine tetrahydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.3418 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: Jun 9, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3418 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→34.96 Å / Num. obs: 1535 / % possible obs: 97.9 % / Redundancy: 31.3 % / Biso Wilson estimate: 106.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.014 / Rrim(I) all: 0.065 / Χ2: 1.05 / Net I/σ(I): 35.8 |
Reflection shell | Resolution: 2.95→3.19 Å / Rmerge(I) obs: 0.998 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 291 / CC1/2: 0.962 / Rpim(I) all: 0.184 / Rrim(I) all: 1.016 / Χ2: 0.97 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ROS Resolution: 3.2→34.96 Å / SU ML: 0.4007 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.9057 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: 117.82 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→34.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.31 Å
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