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Yorodumi- PDB-4beb: MUTANT (K220E) OF THE HSDR SUBUNIT OF THE ECOR124I RESTRICTION EN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4beb | |||||||||
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Title | MUTANT (K220E) 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: 2.989 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 | 4beb.cif.gz | 686.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4beb.ent.gz | 553 KB | Display | PDB format |
PDBx/mmJSON format | 4beb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4beb_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4beb_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4beb_validation.xml.gz | 109.9 KB | Display | |
Data in CIF | 4beb_validation.cif.gz | 146.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/4beb ftp://data.pdbj.org/pub/pdb/validation_reports/be/4beb | HTTPS FTP |
-Related structure data
Related structure data | 4be7C 4becC 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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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 120278.797 Da / Num. of mol.: 4 / 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 | ChemComp-MG / #3: Chemical | ChemComp-ATP / |
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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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 6UL PROTEIN MIXED WITH 0.8UL OF 2M NH4F AND 2UL WELL SOLUTION OF 22% W/V PEG4K, 0.1M MES PH 5.7. 20C, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.815 |
Detector | Type: MARRESEARCH MX-555 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.815 Å / Relative weight: 1 |
Reflection | Resolution: 2.989→20 Å / Num. obs: 92081 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 41.12 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.989→3.17 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.7 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2W00 Resolution: 2.989→19.885 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 35.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.989→19.885 Å
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Refine LS restraints |
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LS refinement shell |
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