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Open data
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Basic information
Entry | Database: PDB / ID: 1vde | ||||||
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Title | PI-SCEI, A HOMING ENDONUCLEASE WITH PROTEIN SPLICING ACTIVITY | ||||||
![]() | PI-SCEI | ||||||
![]() | ENDONUCLEASE / HOMING ENDONUCLEASE / PROTEIN SPLICING | ||||||
Function / homology | ![]() Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase complex / protein metabolic process / intein-mediated protein splicing ...Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase complex / protein metabolic process / intein-mediated protein splicing / intron homing / fungal-type vacuole membrane / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / H+-transporting two-sector ATPase / proton transmembrane transport / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Duan, X. / Quiocho, F.A. | ||||||
![]() | ![]() Title: Crystal structure of PI-SceI, a homing endonuclease with protein splicing activity. Authors: Duan, X. / Gimble, F.S. / Quiocho, F.A. #1: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184.5 KB | Display | ![]() |
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PDB format | ![]() | 147 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 379.4 KB | Display | ![]() |
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Full document | ![]() | 421.3 KB | Display | |
Data in XML | ![]() | 23.3 KB | Display | |
Data in CIF | ![]() | 36 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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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: |
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Components
#1: Protein | Mass: 51003.895 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: PT7PI-SCEI ESARC / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() | |||||||||
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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