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Yorodumi- PDB-4bec: MUTANT (K220A) OF THE HSDR SUBUNIT OF THE ECOR124I RESTRICTION EN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bec | ||||||
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Title | MUTANT (K220A) OF THE HSDR SUBUNIT OF THE ECOR124I RESTRICTION ENZYME IN COMPLEX WITH ATP | ||||||
Components | TYPE I RESTRICTION ENZYME HSDR | ||||||
Keywords | HYDROLASE / DNA MODIFICATION | ||||||
Function / homology | Function and homology information type I site-specific deoxyribonuclease / type I site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding / ATP binding Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å | ||||||
Authors | Csefalvay, E. / Lapkouski, M. / Guzanova, A. / Csefalvay, L. / Baikova, T. / Shevelev, I. / Janscak, P. / Smatanova, I.K. / Panjikar, S. / Carey, J. ...Csefalvay, E. / Lapkouski, M. / Guzanova, A. / Csefalvay, L. / Baikova, T. / Shevelev, I. / Janscak, P. / Smatanova, I.K. / Panjikar, S. / Carey, J. / Weiserova, M. / Ettrich, R. | ||||||
Citation | Journal: Plos One / Year: 2015 Title: Functional Coupling of Duplex Translocation to DNA Cleavage in a Type I Restriction Enzyme. Authors: Csefalvay, E. / Lapkouski, M. / Guzanova, A. / Csefalvay, L. / Baikova, T. / Shevelev, I. / Bialevich, V. / Shamayeva, K. / Janscak, P. / Kuta Smatanova, I. / Panjikar, S. / Carey, J. / ...Authors: Csefalvay, E. / Lapkouski, M. / Guzanova, A. / Csefalvay, L. / Baikova, T. / Shevelev, I. / Bialevich, V. / Shamayeva, K. / Janscak, P. / Kuta Smatanova, I. / Panjikar, S. / Carey, J. / Weiserova, M. / Ettrich, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bec.cif.gz | 356.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bec.ent.gz | 281.6 KB | Display | PDB format |
PDBx/mmJSON format | 4bec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/4bec ftp://data.pdbj.org/pub/pdb/validation_reports/be/4bec | HTTPS FTP |
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-Related structure data
Related structure data | 4be7C 4bebC 2w00S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 120220.781 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q304R3, UniProt: P10486*PLUS, type I site-specific deoxyribonuclease #2: Chemical | #3: Chemical | #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: 2.73 Å3/Da / Density % sol: 55 % / Description: NONE |
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Crystal grow | Details: 5UL PROTEIN (WITH 5 MM ATP) MIXED WITH 2 UL WELL SOLUTION OF 13% W/V PEG4K, 22% GLYCEROL, 0.08M MES PH 5.9, 2MM DTT AND 0.7UL NABR |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromator: HOROZONTALLY FOCUSING MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.84 Å / Relative weight: 1 |
Reflection | Resolution: 2.84→18.9 Å / Num. obs: 59509 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.84→2.99 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.3 / % possible all: 87.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2W00 Resolution: 2.84→18.86 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.888 / SU B: 18.29 / SU ML: 0.337 / Cross valid method: THROUGHOUT / ESU R: 2.12 / ESU R Free: 0.404 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.814 Å2
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Refinement step | Cycle: LAST / Resolution: 2.84→18.86 Å
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Refine LS restraints |
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