+Open data
-Basic information
Entry | Database: PDB / ID: 2i3p | ||||||
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Title | K28R mutant of Homing Endonuclease I-CreI | ||||||
Components |
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Keywords | HYDROLASE/DNA / Homing endonulease I-CreI / DNA / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information intron homing / chloroplast / endonuclease activity / Hydrolases; Acting on ester bonds / metal ion binding / identical protein binding Similarity search - Function | ||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Sussman, D. / Rosen, L. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2006 Title: Homing endonuclease I-CreI derivatives with novel DNA target specificities. Authors: Rosen, L.E. / Morrison, H.A. / Masri, S. / Brown, M.J. / Springstubb, B. / Sussman, D. / Stoddard, B.L. / Seligman, L.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i3p.cif.gz | 107.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i3p.ent.gz | 77.5 KB | Display | PDB format |
PDBx/mmJSON format | 2i3p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/2i3p ftp://data.pdbj.org/pub/pdb/validation_reports/i3/2i3p | HTTPS FTP |
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-Related structure data
Related structure data | 2i3qC 1g9yS 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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1 |
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Unit cell |
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Details | The assymetric unit contains one biologically active complex. I-CreI binds the DNA substrate as a homodimer and subsequently cleaves both strands. |
-Components
#1: DNA chain | Mass: 7393.792 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
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#2: DNA chain | Mass: 7344.753 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
#3: Protein | Mass: 17675.328 Da / Num. of mol.: 2 / Mutation: K28R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Plasmid: pI-CreI / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 RIL References: UniProt: P05725, Hydrolases; Acting on ester bonds #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.46 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.5 Details: PEG 400 28%, pH 6.5, VAPOR DIFFUSION, temperature 298K | ||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
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Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 11, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→27.69 Å / Num. obs: 21742 / % possible obs: 96 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.039 / Χ2: 1.462 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.097 / Num. unique all: 1033 / Χ2: 1.424 / % possible all: 93.9 |
-Phasing
Phasing MR | Rfactor: 0.398 / Cor.coef. Fo:Fc: 0.608
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G9Y Resolution: 2.3→27.69 Å / σ(F): 0
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Solvent computation | Bsol: 38.114 Å2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.169 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→27.69 Å
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Xplor file |
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