+Open data
-Basic information
Entry | Database: PDB / ID: 6s16 | |||||||||
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Title | T. thermophilus RuvC in complex with Holliday junction substrate | |||||||||
Components |
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Keywords | HYDROLASE / RuvC resolvase Holliday junction | |||||||||
Function / homology | Function and homology information crossover junction endodeoxyribonuclease / Holliday junction resolvase complex / crossover junction DNA endonuclease activity / DNA recombination / DNA repair / magnesium ion binding / DNA binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Thermus thermophilus (bacteria) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.409 Å | |||||||||
Authors | Gorecka, K.M. / Krepl, M. / Szlachcic, A. / Poznanski, J. / Sponer, J. / Nowotny, M. | |||||||||
Funding support | Czech Republic, 2items
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Citation | Journal: Nat Commun / Year: 2019 Title: RuvC uses dynamic probing of the Holliday junction to achieve sequence specificity and efficient resolution. Authors: Gorecka, K.M. / Krepl, M. / Szlachcic, A. / Poznanski, J. / Sponer, J. / Nowotny, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6s16.cif.gz | 105.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s16.ent.gz | 75.6 KB | Display | PDB format |
PDBx/mmJSON format | 6s16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s1/6s16 ftp://data.pdbj.org/pub/pdb/validation_reports/s1/6s16 | HTTPS FTP |
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-Related structure data
Related structure data | 4ld0S 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 18074.121 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Gene: ruvC, TTHA1090 / Production host: Escherichia coli (E. coli) References: UniProt: Q5SJC4, crossover junction endodeoxyribonuclease |
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-DNA chain , 2 types, 3 molecules CDF
#2: DNA chain | Mass: 10136.518 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
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#3: DNA chain | Mass: 10136.520 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
-Non-polymers , 3 types, 5 molecules
#4: Chemical | ChemComp-NA / |
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#5: Chemical | ChemComp-CL / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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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: 3.38 Å3/Da / Density % sol: 63.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.4 M ammonium phosphate |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.895 Å |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Sep 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.895 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→38.3 Å / Num. obs: 12660 / % possible obs: 99.5 % / Redundancy: 5.6 % / CC1/2: 1 / Rrim(I) all: 0.083 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 3.4→3.5 Å / Num. unique obs: 2003 / CC1/2: 0.717 / Rrim(I) all: 0.11 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LD0 Resolution: 3.409→38.296 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.52
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.409→38.296 Å
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Refine LS restraints |
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LS refinement shell |
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