+Open data
-Basic information
Entry | Database: PDB / ID: 1vde | ||||||
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Title | PI-SCEI, A HOMING ENDONUCLEASE WITH PROTEIN SPLICING ACTIVITY | ||||||
Components | PI-SCEI | ||||||
Keywords | ENDONUCLEASE / HOMING ENDONUCLEASE / PROTEIN SPLICING | ||||||
Function / homology | Function and homology information Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / endosomal lumen acidification / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification ...Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / endosomal lumen acidification / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / intron homing / protein metabolic process / intein-mediated protein splicing / fungal-type vacuole membrane / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / endonuclease activity / Hydrolases; Acting on ester bonds / Golgi membrane / mRNA binding / DNA binding / ATP binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Duan, X. / Quiocho, F.A. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1997 Title: Crystal structure of PI-SceI, a homing endonuclease with protein splicing activity. Authors: Duan, X. / Gimble, F.S. / Quiocho, F.A. #1: Journal: J.Mol.Biol. / Year: 1996 Title: Substrate Recognition and Induced DNA Distortion by the Pi-Scei Endonuclease, an Enzyme Generated by Protein Splicing Authors: Gimble, F.S. / Wang, J. #2: Journal: Nature / Year: 1992 Title: Homing of a DNA Endonuclease Gene by Meiotic Gene Conversion in Saccharomyces Cerevisiae Authors: Gimble, F.S. / Thorner, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vde.cif.gz | 184.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vde.ent.gz | 147 KB | Display | PDB format |
PDBx/mmJSON format | 1vde.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/1vde ftp://data.pdbj.org/pub/pdb/validation_reports/vd/1vde | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.1505, 0.9851, 0.0827), Vector: |
-Components
#1: Protein | Mass: 51003.895 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: PT7PI-SCEI ESARC / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 (DE3) / References: UniProt: P17255, EC: 3.6.1.34 #2: 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: 2.7 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: 4% PEG 6K, 10MM BME, 3MM CDCL2, 1MM MGCL2, 100MM TRIS, PH=8.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: NSLS / Beamline: X4A / Wavelength: 0.9794 / Wavelength: 0.9656, 0.9794 | |||||||||
Detector | Detector: IMAGE PLATE / Date: Sep 1, 1996 | |||||||||
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→15 Å / Num. obs: 77252 / % possible obs: 96.7 % / Observed criterion σ(I): 3 / Redundancy: 3 % / Rsym value: 0.059 / Net I/σ(I): 19.9 | |||||||||
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 11.5 / Rsym value: 0.116 / % possible all: 97.3 | |||||||||
Reflection | *PLUS Lowest resolution: 10 Å / Rmerge(I) obs: 0.06 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / σ(F): 3
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Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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