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Yorodumi- PDB-6t22: N-terminal domain of EcoKMcrA restriction endonuclease (NEco) in ... -
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-Basic information
Entry | Database: PDB / ID: 6t22 | ||||||
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Title | N-terminal domain of EcoKMcrA restriction endonuclease (NEco) in complex with T5hmCGA 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 | ||||||
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 K-12 (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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 | 6t22.cif.gz | 189.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t22.ent.gz | 147.3 KB | Display | PDB format |
PDBx/mmJSON format | 6t22.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6t22_validation.pdf.gz | 457.4 KB | Display | wwPDB validaton report |
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Full document | 6t22_full_validation.pdf.gz | 459.9 KB | Display | |
Data in XML | 6t22_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 6t22_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t2/6t22 ftp://data.pdbj.org/pub/pdb/validation_reports/t2/6t22 | HTTPS FTP |
-Related structure data
Related structure data | 6r64C 6t21C 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 on special symmetry positions |
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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 K-12 (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: 3025.005 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: 3123.080 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) #4: Water | ChemComp-HOH / | 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: 3.09 Å3/Da / Density % sol: 60.15 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.8 ul of protein-DNA solution (436:523 uM) was mixed with 2.2 ul of the F1 condition of the PACT premier crystal screen (MDL) (0.2 M Sodium fluoride, 0.1 M Bis-Tris propane, pH 6.5, 20% PEG ...Details: 1.8 ul of protein-DNA solution (436:523 uM) was mixed with 2.2 ul of the F1 condition of the PACT premier crystal screen (MDL) (0.2 M Sodium fluoride, 0.1 M Bis-Tris propane, pH 6.5, 20% PEG 3350) and cryo-protected with an addition of 25% glycerol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9195 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9195 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→33.54 Å / Num. obs: 30298 / % possible obs: 99.2 % / Redundancy: 35.8 % / Biso Wilson estimate: 55.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.086 / Net I/σ(I): 38.15 |
Reflection shell | Resolution: 2.21→2.34 Å / Redundancy: 20.8 % / Rmerge(I) obs: 1.761 / Mean I/σ(I) obs: 1.91 / Num. unique obs: 4597 / CC1/2: 0.734 / Rrim(I) all: 1.802 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GHC Resolution: 2.21→33.54 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / SU B: 8.998 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.163 Details: HYDROGEN ATOMS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS REFINEMENT HAS BEEN USED. U VALUES : WITH TLS ADDED. THE CLUSTERS OF SOLVENT MOLECULES BETWEEN RESIDUES 46 AND 94 AND NEXT TO ...Details: HYDROGEN ATOMS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS REFINEMENT HAS BEEN USED. U VALUES : WITH TLS ADDED. THE CLUSTERS OF SOLVENT MOLECULES BETWEEN RESIDUES 46 AND 94 AND NEXT TO RESIDUE 54 OF CHAIN B LIKELY CORRESPOND TO DISORDERED GLYCEROL MOLECULES. THE ELECTRON DENSITY IS NOT DEFINED ENOUGH TO UNAMBIGUOUSLY MODEL THEM.
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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: 158.21 Å2 / Biso mean: 53.522 Å2 / Biso min: 35.08 Å2
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Refinement step | Cycle: final / Resolution: 2.21→33.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.21→2.26 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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