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Yorodumi- PDB-6r64: N-terminal domain of modification dependent EcoKMcrA restriction ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r64 | ||||||
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Title | N-terminal domain of modification dependent EcoKMcrA restriction endonuclease (NEco) in complex with C5mCGG target sequence | ||||||
Components |
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Keywords | HYDROLASE / EcoKMcrA / NEco / N-TERMINAL DOMAIN / MODIFICATION DEPENDENT RESTRICTION / 5-METHYLCYTOSINE / 5MC / 5-HYDROXYMETHYLCYTOSINE / 5HMC / HNH ENDONUCLEASE / BBA-ME NUCLEASE / ScoMcrA | ||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / DNA restriction-modification system / methyl-CpG binding / endonuclease activity / zinc ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli K12 (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å | ||||||
Authors | Slyvka, A. / Zagorskaite, E. / Czapinska, H. / Sasnauskas, G. / Bochtler, M. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Crystal structure of the EcoKMcrA N-terminal domain (NEco): recognition of modified cytosine bases without flipping. Authors: Slyvka, A. / Zagorskaite, E. / Czapinska, H. / Sasnauskas, G. / Bochtler, M. #1: Journal: Nucleic Acids Res. / Year: 2018 Title: Activity and structure of EcoKMcrA. Authors: Czapinska, H. / Kowalska, M. / Zagorskaite, E. / Manakova, E. / Slyvka, A. / Xu, S.Y. / Siksnys, V. / Sasnauskas, G. / Bochtler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r64.cif.gz | 99.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r64.ent.gz | 72.4 KB | Display | PDB format |
PDBx/mmJSON format | 6r64.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6r64_validation.pdf.gz | 450.8 KB | Display | wwPDB validaton report |
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Full document | 6r64_full_validation.pdf.gz | 454 KB | Display | |
Data in XML | 6r64_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 6r64_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/6r64 ftp://data.pdbj.org/pub/pdb/validation_reports/r6/6r64 | HTTPS FTP |
-Related structure data
Related structure data | 6t21C 6t22C 6ghcS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17368.604 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Gene: mcrA, rglA, b1159, JW1145 / Plasmid: PET15BM / Production host: Escherichia coli (E. coli) References: UniProt: P24200, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters #2: DNA chain | Mass: 3009.994 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 3108.069 Da / Num. of mol.: 2 / 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: 8.29 Å3/Da / Density % sol: 85.17 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: NEco in the crystallization buffer (20 mM Tris-HCl, pH 8.0, 0.1 M NaCl, 1 mM EDTA, 2 mM DTT) was concentrated to 8.7 mg/ml and mixed in the 1:1.2 ratio with 10-mer TCAC5mCGGTTC ...Details: NEco in the crystallization buffer (20 mM Tris-HCl, pH 8.0, 0.1 M NaCl, 1 mM EDTA, 2 mM DTT) was concentrated to 8.7 mg/ml and mixed in the 1:1.2 ratio with 10-mer TCAC5mCGGTTC oligonucleotide, annealed to its complementary GAAC5mCGTGA strand. Crystals were grown by mixing 1.8 ul of the protein-DNA mixture with 2.2 ul of the condition F1 of the PACT premier crystal screen (MDL) (0.2 M NaF, 0.1 M Bis-Tris propane, pH 6.5, 20% PEG3350). Crystals were cryo-protected by the addition of 25% glycerol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2018 |
Radiation | Monochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→45.55 Å / Num. obs: 17671 / % possible obs: 99.8 % / Redundancy: 16 % / Biso Wilson estimate: 50.9 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.23 / Rsym value: 0.223 / Net I/σ(I): 12.52 |
Reflection shell | Resolution: 2.64→2.8 Å / Redundancy: 16.7 % / Mean I/σ(I) obs: 1.97 / Num. unique obs: 2761 / CC1/2: 0.764 / Rrim(I) all: 1.509 / Rsym value: 1.463 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 6GHC Resolution: 2.64→45.55 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.926 / SU B: 11.193 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.492 / ESU R Free: 0.273 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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 mean: 53.738 Å2
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Refinement step | Cycle: LAST / Resolution: 2.64→45.55 Å
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Refine LS restraints |
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