+Open data
-Basic information
Entry | Database: PDB / ID: 1mow | ||||||
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Title | E-DreI | ||||||
Components |
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Keywords | Hydrolase/DNA / LAGLIDADG / homing / engineering / design / endonuclease / Hydrolase-DNA COMPLEX | ||||||
Function / homology | Function and homology information intein-mediated protein splicing / intron homing / chloroplast / endonuclease activity / Hydrolases; Acting on ester bonds / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Desulfurococcus mobilis (archaea) Chlamydomonas reinhardtii (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Chevalier, B.S. / Kortemme, T. / Chadsey, M.S. / Baker, D. / Monnat Jr., R.J. / Stoddard, B.L. | ||||||
Citation | Journal: Mol.Cell / Year: 2002 Title: Design, Activity and Structure of a Highly Specific Artificial Endonuclease Authors: Chevalier, B.S. / Kortemme, T. / Chadsey, M.S. / Baker, D. / Monnat Jr., R.J. / Stoddard, B.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mow.cif.gz | 303 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mow.ent.gz | 222.8 KB | Display | PDB format |
PDBx/mmJSON format | 1mow.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mow_validation.pdf.gz | 538.4 KB | Display | wwPDB validaton report |
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Full document | 1mow_full_validation.pdf.gz | 570.8 KB | Display | |
Data in XML | 1mow_validation.xml.gz | 46.9 KB | Display | |
Data in CIF | 1mow_validation.cif.gz | 67.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mo/1mow ftp://data.pdbj.org/pub/pdb/validation_reports/mo/1mow | HTTPS FTP |
-Related structure data
Related structure data | 1g9zS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
-DNA chain , 2 types, 8 molecules BEHKCFIL
#1: DNA chain | Mass: 7001.524 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: DNA target site (top strand) #2: DNA chain | Mass: 7121.597 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: DNA target site (bottom strand) |
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-Protein , 1 types, 4 molecules ADGJ
#3: Protein | Mass: 30025.645 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: The chimera contains large domain of I-DmoI fused to one subunit of I-CreI: E-DreI protein Source: (gene. exp.) Desulfurococcus mobilis (archaea), (gene. exp.) Chlamydomonas reinhardtii (plant) Genus: Desulfurococcus, Chlamydomonas / Species: , / Strain: , / Plasmid: pDre16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3] References: UniProt: p21505, UniProt: p05725, UniProt: P21505*PLUS, Hydrolases; Acting on ester bonds |
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-Non-polymers , 4 types, 488 molecules
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-SO4 / #7: 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: 4.04 Å3/Da / Density % sol: 69.31 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: ammonium sulphate, MES, magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 10, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 91595 / % possible obs: 99.9 % / Redundancy: 3 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.081 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 91688 / % possible obs: 99 % / Num. measured all: 305673 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: E-DreI computational model; I-CreI/DNA complex (RCSB 1G9Z) Resolution: 2.4→19.86 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1748854.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 84.5375 Å2 / ksol: 0.363178 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor Rfree: 0.256 / Rfactor Rwork: 0.236 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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