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Yorodumi- PDB-1g9z: LAGLIDADG HOMING ENDONUCLEASE I-CREI / DNA PRODUCT COMPLEX WITH M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g9z | ||||||
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Title | LAGLIDADG HOMING ENDONUCLEASE I-CREI / DNA PRODUCT COMPLEX WITH MAGNESIUM | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 | 1g9z.cif.gz | 127.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g9z.ent.gz | 91.5 KB | Display | PDB format |
PDBx/mmJSON format | 1g9z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/1g9z ftp://data.pdbj.org/pub/pdb/validation_reports/g9/1g9z | HTTPS FTP |
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-Related structure data
Related structure data | 1g9yC 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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Details | pseudo-palindromic homing site (wildtype sequence) is observed in both possible orientations within the crystal; non-palindromic bases are averaged in final refined model, and coordinates of alternate DNA orientation are available by request from corresponding author. |
-Components
-DNA chain , 4 types, 4 molecules CDEF
#1: DNA chain | Mass: 4313.831 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3060.016 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 4224.769 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: DNA chain | Mass: 3051.001 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 1 types, 2 molecules AB
#5: Protein | Mass: 17516.121 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) Gene: ENCODED BY AN ORF WITHIN CR.LSU INTRON OF CHLOROPLAST 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 |
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-Non-polymers , 2 types, 860 molecules
#6: Chemical | #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: 2.56 Å3/Da / Density % sol: 52.02 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 30% PEG400, PH 6.5, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||
Components of the solutions | Name: PEG400 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS PH range low: 6.6 / PH range high: 3 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 |
Detector | Type: ADSC / Detector: CCD / Date: Apr 1, 2000 / Details: SLITS |
Radiation | Monochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 44925 / % possible obs: 95.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 3.8 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 1.8→1.89 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.185 / Rsym value: 18.5 / % possible all: 75.3 |
Reflection shell | *PLUS % possible obs: 75.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CRE/DNA (PDB ENTRY 1BP7) Resolution: 1.8→19.92 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1072916.28 / 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: 49.5928 Å2 / ksol: 0.296075 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.89 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 7
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Xplor file |
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Refine LS restraints | *PLUS
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