+Open data
-Basic information
Entry | Database: PDB / ID: 8cty | ||||||
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Title | 12-mer DNA structure of ExBIM bound to RNase-H | ||||||
Components |
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Keywords | DNA / alkylation / base stacking / DNA damage / H-bonding / O6-methyl-2'-deoxyguanosine / ExBIM | ||||||
Function / homology | Function and homology information ribonuclease H / RNA-DNA hybrid ribonuclease activity / nucleic acid binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Halalkalibacterium halodurans (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Pallan, P.S. / Egli, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Chem.Res.Toxicol. / Year: 2022 Title: Conformation and Pairing Properties of an O 6 -Methyl-2'-deoxyguanosine-Directed Benzimidazole Nucleoside Analog in Duplex DNA. Authors: Kellum Jr., A.H. / Pallan, P.S. / Nilforoushan, A. / Sturla, S.J. / Stone, M.P. / Egli, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cty.cif.gz | 267.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cty.ent.gz | 210.3 KB | Display | PDB format |
PDBx/mmJSON format | 8cty.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ct/8cty ftp://data.pdbj.org/pub/pdb/validation_reports/ct/8cty | HTTPS FTP |
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-Related structure data
Related structure data | 8ctzC 8cu0C 3ey1S 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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2 |
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3 |
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Unit cell |
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-Components
-Protein / DNA chain , 2 types, 14 molecules ABCDEFGHIJKLMN
#1: Protein | Mass: 16329.478 Da / Num. of mol.: 8 / Mutation: D132N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halalkalibacterium halodurans (bacteria) Gene: rnhA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KEI9, ribonuclease H #2: DNA chain | Mass: 3720.485 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 7 types, 287 molecules
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-PEG / | #7: Chemical | ChemComp-NA / | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.4 Å3/Da / Density % sol: 48.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES sodium pH = 7.5, 10% v/v 2-propanol and 20% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→32.73 Å / Num. obs: 61160 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 38.07 Å2 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.053 / Net I/σ(I): 3.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.1 % / Rmerge(I) obs: 1.043 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 5899 / CC1/2: 0.386 / Rpim(I) all: 0.683 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3EY1 Resolution: 2.3→32.73 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 26.72 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.14 Å2 / Biso mean: 42.7127 Å2 / Biso min: 18.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→32.73 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22
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