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- PDB-6gce: DNA binding domain of restriction endonuclease McrBC in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gce | ||||||
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Title | DNA binding domain of restriction endonuclease McrBC in complex with 5-formylcytosine DNA | ||||||
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![]() | DNA BINDING PROTEIN / 5-formylcytosine / restriction endonuclease / McrBC / base flipping | ||||||
Function / homology | ![]() restriction endodeoxyribonuclease activity / endonuclease complex / double-stranded methylated DNA binding / hemi-methylated DNA-binding / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / DNA restriction-modification system / DNA catabolic process / endonuclease activity / GTPase activity / GTP binding ...restriction endodeoxyribonuclease activity / endonuclease complex / double-stranded methylated DNA binding / hemi-methylated DNA-binding / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / DNA restriction-modification system / DNA catabolic process / endonuclease activity / GTPase activity / GTP binding / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sasnauskas, G. | ||||||
Funding support | Lithuania, 1items
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![]() | ![]() Title: Recognition of modified cytosine variants by the DNA-binding domain of methyl-directed endonuclease McrBC. Authors: Zagorskaite, E. / Manakova, E. / Sasnauskas, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 195.5 KB | Display | ![]() |
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PDB format | ![]() | 153.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.4 KB | Display | ![]() |
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Full document | ![]() | 446.3 KB | Display | |
Data in XML | ![]() | 18.6 KB | Display | |
Data in CIF | ![]() | 28.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gcdC ![]() 6gcfC ![]() 3sscS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19659.920 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P15005, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters #2: DNA chain | | Mass: 3642.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | | Mass: 3712.430 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M LiCl, 22% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.001 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→35.09 Å / Num. obs: 92903 / % possible obs: 99.62 % / Redundancy: 6.3 % / Biso Wilson estimate: 29.46 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 17.15 |
Reflection shell | Resolution: 1.6→1.657 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 9718 / % possible all: 99.92 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ssc Resolution: 1.6→35.089 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.86 / Phase error: 22.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→35.089 Å
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Refine LS restraints |
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LS refinement shell |
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