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Yorodumi- PDB-2w00: Crystal structure of the HsdR subunit of the EcoR124I restriction... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w00 | ||||||
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Title | Crystal structure of the HsdR subunit of the EcoR124I restriction enzyme in complex with ATP | ||||||
Components | HSDR | ||||||
Keywords | HYDROLASE / ATP-BINDING / DNA-BINDING / RESTRICTION SYSTEM / HELICASE / R.ECOR124I / NUCLEOTIDE-BINDING / TYPE I RESTRICTION-MODIFICATION ENZYME | ||||||
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 / SAD / Resolution: 2.6 Å | ||||||
Authors | Lapkouski, M. / Panjikar, S. / Kuta Smatanova, I. / Ettrich, R. / Csefalvay, E. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2009 Title: Structure of the Motor Subunit of Type I Restriction-Modification Complex Ecor124I. Authors: Lapkouski, M. / Panjikar, S. / Janscak, P. / Smatanova, I.K. / Carey, J. / Ettrich, R. / Csefalvay, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w00.cif.gz | 368.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w00.ent.gz | 307.1 KB | Display | PDB format |
PDBx/mmJSON format | 2w00.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w00_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 2w00_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 2w00_validation.xml.gz | 71.1 KB | Display | |
Data in CIF | 2w00_validation.cif.gz | 99.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/2w00 ftp://data.pdbj.org/pub/pdb/validation_reports/w0/2w00 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-1, -0.0031, -0.0037), Vector: |
-Components
#1: Protein | Mass: 120982.328 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: B834(DE3) / Plasmid: PTRC124 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) References: UniProt: Q304R3, UniProt: P10486*PLUS, type I site-specific deoxyribonuclease #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | SEQUENCE TAKEN FROM THE NCBI PROTEIN DATABASE | |
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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: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 1 UL OF PROTEIN IN 20 MM PHOSPHATE PH 7.5, 100 MM KCL, 5 MM ATP WAS MIXED WITH 2 UL OF RESERVOIR, CONTAINING 0.2 M LI2SO4, 8 % PEG 20K, 8 % PEG 550 MME, 1.5 MM DTT, 277 K, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9784 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 20, 2006 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL SI HORYSONTAL FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9784 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 80316 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 5.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.6→19.97 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.911 / SU B: 19.401 / SU ML: 0.215 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.469 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.95 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→19.97 Å
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Refine LS restraints |
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