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Yorodumi- PDB-3lx6: Crystal structure of putative dna cytosine methylase from shigell... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lx6 | ||||||
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Title | Crystal structure of putative dna cytosine methylase from shigella flexneri 2a str. 2457T | ||||||
Components | Cytosine-specific methyltransferase | ||||||
Keywords | TRANSFERASE / structural genomics / dcm / Restriction system / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | DNA Methylase; Chain A, domain 2 - #30 / DNA Methylase; Chain A, domain 2 / Vaccinia Virus protein VP39 / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / : Function and homology information | ||||||
Biological species | Shigella flexneri 2a (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.29 Å | ||||||
Authors | Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of putative dna cytosine methylase from shigella flexneri 2a str. 2457T Authors: Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lx6.cif.gz | 150.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lx6.ent.gz | 123 KB | Display | PDB format |
PDBx/mmJSON format | 3lx6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/3lx6 ftp://data.pdbj.org/pub/pdb/validation_reports/lx/3lx6 | HTTPS FTP |
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-Related 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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Details | unknown |
-Components
#1: Protein | Mass: 47123.414 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri 2a (bacteria) / Strain: 2457T / Gene: dcm, S2100, SF2005, SF2457T_1495 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: E3Y0J2, DNA (cytosine-5-)-methyltransferase #2: 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: 2.72 Å3/Da / Density % sol: 54.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M Hepes pH 7.5, 10% PEG 8K, 8% Ethylene Glycol, Vapor diffusion, Sitting drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9793 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.29→50 Å / Num. obs: 43909 / % possible obs: 96.8 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.083 / Χ2: 1.366 / Net I/σ(I): 12.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.29→31.26 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.302 / WRfactor Rwork: 0.257 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.763 / SU B: 18.944 / SU ML: 0.211 / SU R Cruickshank DPI: 0.323 / SU Rfree: 0.254 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.323 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.47 Å2 / Biso mean: 32.744 Å2 / Biso min: 13.02 Å2
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Refinement step | Cycle: LAST / Resolution: 2.29→31.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.292→2.351 Å / Total num. of bins used: 20
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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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