+Open data
-Basic information
Entry | Database: PDB / ID: 7z7z | |||||||||
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Title | REP-related Chom18 variant with double TA base pair | |||||||||
Components | Chom18-TA 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Svoboda, J. / Schneider, B. / Berdar, D. / Kolenko, P. | |||||||||
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 | 7z7z.cif.gz | 24.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z7z.ent.gz | 11.8 KB | Display | PDB format |
PDBx/mmJSON format | 7z7z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z7z_validation.pdf.gz | 372.4 KB | Display | wwPDB validaton report |
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Full document | 7z7z_full_validation.pdf.gz | 372.4 KB | Display | |
Data in XML | 7z7z_validation.xml.gz | 2.4 KB | Display | |
Data in CIF | 7z7z_validation.cif.gz | 2.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/7z7z ftp://data.pdbj.org/pub/pdb/validation_reports/z7/7z7z | HTTPS FTP |
-Related structure data
Related structure data | 7z7kC 7z7lC 7z7mC 7z7uC 7z7wC 7z7yC 7z81C 7z82C 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: 5518.554 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: 3.03 Å3/Da / Density % sol: 59.39 % |
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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: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2021 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→45.17 Å / Num. obs: 2394 / % possible obs: 100 % / Redundancy: 11.3 % / Biso Wilson estimate: 104.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.015 / Rrim(I) all: 0.046 / Χ2: 1.07 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.6→2.73 Å / Redundancy: 11.7 % / Rmerge(I) obs: 1.596 / Mean I/σ(I) obs: 2 / Num. unique obs: 308 / CC1/2: 0.618 / Rpim(I) all: 0.483 / Rrim(I) all: 1.67 / Χ2: 1.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ROS Resolution: 2.9→35.4 Å / SU ML: 0.5398 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.0951 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: 101.88 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→35.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.99 Å
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