+Open data
-Basic information
Entry | Database: PDB / ID: 6g3b | |||||||||||||||||||||
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Title | AvaII restriction endonuclease in complex with an RNA/DNA hybrid | |||||||||||||||||||||
Components |
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Keywords | HYDROLASE / RESTRICTION ENDONUCLEASE / SCANNING COMPLEX / RNA/DNA HYBRID / RNA/DNA HETERODUPLEX / A-DNA | |||||||||||||||||||||
Function / homology | Function and homology information type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding / metal ion binding Similarity search - Function | |||||||||||||||||||||
Biological species | Nostoc sp. PCC 7120 (bacteria) synthetic construct (others) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | |||||||||||||||||||||
Authors | Kisiala, M. / Kowalska, M. / Czapinska, H. / Bochtler, M. | |||||||||||||||||||||
Funding support | Poland, 6items
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Citation | Journal: Nucleic Acids Res. / Year: 2020 Title: Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation Authors: Kisiala, M. / Kowalska, M. / Pastor, M. / Korza, H. / Czapinska, H. / Bochtler, M. #1: Journal: Nucleic Acids Res. / Year: 2010 Title: Sequence-specific cleavage of RNA by Type II restriction enzymes. Authors: Murray, I.A. / Stickel, S.K. / Roberts, R.J. #2: Journal: J. Biol. Chem. / Year: 2005 Title: Crystal structures of type II restriction endonuclease EcoO109I and its complex with cognate DNA. Authors: Hashimoto, H. / Shimizu, T. / Imasaki, T. / Kato, M. / Shichijo, N. / Kita, K. / Sato, M. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g3b.cif.gz | 251 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g3b.ent.gz | 200.6 KB | Display | PDB format |
PDBx/mmJSON format | 6g3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6g3b_validation.pdf.gz | 464 KB | Display | wwPDB validaton report |
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Full document | 6g3b_full_validation.pdf.gz | 465.2 KB | Display | |
Data in XML | 6g3b_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 6g3b_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/6g3b ftp://data.pdbj.org/pub/pdb/validation_reports/g3/6g3b | HTTPS FTP |
-Related structure data
Related structure data | |
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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
#1: Protein | Mass: 27161.797 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. PCC 7120 (bacteria) / Gene: alr0933 / Production host: Escherichia coli (E. coli) / Variant (production host): ER2566 / References: UniProt: Q8YYB7 #2: RNA chain | | Mass: 3546.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | | Mass: 3309.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #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: 2.65 Å3/Da / Density % sol: 53.59 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10% W/V PEG 20000, 20% V/V PEG MME 550, 0.02 M Na-Formate; 0.02 M NH4-Acetate; 0.02 M Na3-Citrate; 0.02 M NaK-Tartrate (racemic); 0.02 M Na-Oxamate AND 0.1 M MOPS/HEPES-NA, PH 7.5, GLYCEROL ...Details: 10% W/V PEG 20000, 20% V/V PEG MME 550, 0.02 M Na-Formate; 0.02 M NH4-Acetate; 0.02 M Na3-Citrate; 0.02 M NaK-Tartrate (racemic); 0.02 M Na-Oxamate AND 0.1 M MOPS/HEPES-NA, PH 7.5, GLYCEROL WAS ADDED FOR CRYOPROTECTION PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.2782 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2013 |
Radiation | Monochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2782 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→52.025 Å / Num. obs: 53209 / % possible obs: 95.4 % / Redundancy: 2.6 % / Biso Wilson estimate: 42.229 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.051 / Rsym value: 0.041 / Net I/σ(I): 12.96 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.86 / Num. unique obs: 4000 / CC1/2: 0.57 / Rrim(I) all: 0.798 / Rsym value: 0.638 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→52.025 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.85 Details: The register and the strand assignment of the RNA/DNA heteroduplex is unsure. It is plausible that the observed density corresponds to the average of the heteroduplexes bound in multiple ...Details: The register and the strand assignment of the RNA/DNA heteroduplex is unsure. It is plausible that the observed density corresponds to the average of the heteroduplexes bound in multiple different registers. The sequence assignment is based on the known sequence specificity of AvaII endonuclease but remains very tentative. The density for the 166-176 fragments of both enzyme protomers is very poor. TLS refinement has been used. Hydrogens have been added in the riding positions. Group B-factor refinement has been used for the RNA/DNA molecule.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→52.025 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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