+Open data
-Basic information
Entry | Database: PDB / ID: 1g9y | ||||||
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Title | HOMING ENDONUCLEASE I-CREI / DNA SUBSTRATE COMPLEX WITH CALCIUM | ||||||
Components |
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Keywords | HYDROLASE/DNA / LAGLIDADG / homing endonuclease / nuclease mechanism / Group I intron / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information intron homing / chloroplast / endonuclease activity / Hydrolases; Acting on ester bonds / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Chevalier, B. / Monnat, R.J. / Stoddard, B.L. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites. Authors: Chevalier, B.S. / 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 | 1g9y.cif.gz | 115.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g9y.ent.gz | 82.6 KB | Display | PDB format |
PDBx/mmJSON format | 1g9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g9y_validation.pdf.gz | 382.9 KB | Display | wwPDB validaton report |
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Full document | 1g9y_full_validation.pdf.gz | 395.1 KB | Display | |
Data in XML | 1g9y_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 1g9y_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/1g9y ftp://data.pdbj.org/pub/pdb/validation_reports/g9/1g9y | HTTPS FTP |
-Related structure data
Related structure data | 1g9zC 1bp7S 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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-Components
#1: DNA chain | Mass: 7320.728 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
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#2: DNA chain | Mass: 7418.805 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
#3: Protein | Mass: 17516.121 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CR.LSU INTRON OF CHOROPLAST 23S RRNA GENE / Plasmid: PI-CREI / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) 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: 2.57 Å3/Da / Density % sol: 52.08 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 25% PEG 400, pH 6.5, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||
Components of the solutions | Name: PEG 400 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS PH range low: 6.6 / PH range high: 6.3 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: ADSC / Detector: CCD / Date: May 1, 2000 / Details: MIRRORS |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 30037 / % possible obs: 91.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 5.5 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.36 / Rsym value: 36 / % possible all: 81.7 |
Reflection shell | *PLUS % possible obs: 81.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CRE/DNA (PDB ENTRY 1BP7) Resolution: 2.05→26.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 922399.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: The structure contains an average of the two possible orientations of the DNA substrate (see paper). This PDB entry contains only one DNA orientation for clarity.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.7483 Å2 / ksol: 0.297407 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→26.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.09 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 20
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Xplor file |
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Refine LS restraints | *PLUS
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