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- PDB-6ymg: VcaM4I restriction endonuclease in complex with 5mC-modified dsDNA -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ymg | ||||||
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Title | VcaM4I restriction endonuclease in complex with 5mC-modified dsDNA | ||||||
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![]() | HYDROLASE / PUA superfamily / EVE domain / DNA endonuclease / modification-dependent restriction endonuclease / MDRE / 5-hydroxymethylcytosine / 5-methylcytosine | ||||||
Function / homology | HNH endonuclease / HNH nuclease / endonuclease activity / DNA / DNA (> 10) / HNH endonuclease![]() | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pastor, M. / Czapinska, H. / Lutz, T. / Helbrecht, I. / Xu, S. / Bochtler, M. | ||||||
![]() | ![]() Title: Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA. Authors: Pastor, M. / Czapinska, H. / Helbrecht, I. / Krakowska, K. / Lutz, T. / Xu, S.Y. / Bochtler, M. #1: Journal: Nucleic Acids Res. / Year: 2019 Title: A protein architecture guided screen for modification dependent restriction endonucleases. Authors: Lutz, T. / Flodman, K. / Copelas, A. / Czapinska, H. / Mabuchi, M. / Fomenkov, A. / He, X. / Bochtler, M. / Xu, S.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 310.8 KB | Display | ![]() |
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PDB format | ![]() | 250.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465 KB | Display | ![]() |
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Full document | ![]() | 467.3 KB | Display | |
Data in XML | ![]() | 25 KB | Display | |
Data in CIF | ![]() | 34.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6yexSC ![]() 6yjbC ![]() 6ykfC S: Starting model for refinement C: citing same article ( |
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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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35390.543 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-DNA chain , 2 types, 4 molecules CEDF
#2: DNA chain | Mass: 3348.213 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) #3: DNA chain | Mass: 3374.210 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
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-Non-polymers , 3 types, 96 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CL / | ||
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#5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.65 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.25 Details: Reservoir solution: 1.2 M (NH4)2SO4 , 0.1 M MES pH 5.25; protein:DNA solution: 0.3 M NaCl, 15 mM Tris-HCl pH 8.5 and 1 mM TCEP. For cryo-protection the reservoir solution was diluted with ...Details: Reservoir solution: 1.2 M (NH4)2SO4 , 0.1 M MES pH 5.25; protein:DNA solution: 0.3 M NaCl, 15 mM Tris-HCl pH 8.5 and 1 mM TCEP. For cryo-protection the reservoir solution was diluted with glycerol to achieve 30% concentration. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 3.14→49.1 Å / Num. obs: 20874 / % possible obs: 92.8 % / Redundancy: 9.6 % / Biso Wilson estimate: 54.3 Å2 / CC1/2: 0.991 / Rrim(I) all: 0.227 / Rsym value: 0.215 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 3.14→3.33 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 0.89 / Num. unique obs: 2591 / CC1/2: 0.306 / Rrim(I) all: 1.641 / Rsym value: 1.521 / % possible all: 74.4 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 6YEX Resolution: 3.14→49.1 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.881 / SU B: 65.356 / SU ML: 0.464 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.482 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. THE IDENTITY OF THE SOLVENT MOLECULES HAS BEEN ASSIGNED TENTATIVELY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 182.33 Å2 / Biso mean: 71.579 Å2 / Biso min: 22.18 Å2
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Refinement step | Cycle: final / Resolution: 3.14→49.1 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 3.143→3.312 Å / Rfactor Rfree error: 0
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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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