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Open data
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Basic information
Entry | Database: PDB / ID: 1ef0 | ||||||
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Title | CRYSTAL STRUCTURE OF PI-SCEI MINIPRECURSOR | ||||||
![]() | PI-SCEI ENDONUCLEASE | ||||||
![]() | HYDROLASE / endonuclease / protein splicing / mini-precursor | ||||||
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 / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / fungal-type vacuole membrane / 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 | ![]() ![]() | ||||||
![]() | Poland, B.W. / Xu, M.-Q. / Quiocho, F.A. | ||||||
![]() | ![]() Title: Structural insights into the protein splicing mechanism of PI-SceI. Authors: Poland, B.W. / Xu, M.Q. / Quiocho, F.A. #1: ![]() Title: Crystal Structure of PI-SceI, a Homing Endonuclease with Protein Splicing Activity Authors: Duan, X. / Gimble, F.S. / Quiocho, F.A. #2: ![]() Title: Protein Splicing Converts the Yeast TFP1 Gene Product to the 69-kD Subunit of the Vacuolar H+-Adenosine Triphosphatase Authors: Kane, P.M. / Yamashiro, C.T. / Wolczyk, D.F. / Neff, N. / Goebl, M. / Stevens, T.H. #3: ![]() Title: The chemical basis of protein splicing. Authors: Paulus, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 179.6 KB | Display | ![]() |
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PDB format | ![]() | 142.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444 KB | Display | ![]() |
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Full document | ![]() | 477.7 KB | Display | |
Data in XML | ![]() | 38 KB | Display | |
Data in CIF | ![]() | 53.9 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 51803.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: FROM THE VACUOLAR ATPASE SUBUNIT Source: (gene. exp.) ![]() ![]() Plasmid: PVMA29 / Production host: ![]() ![]() References: GenBank: 172907, UniProt: P17255*PLUS, EC: 3.6.1.34 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.93 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 3350, Cadmium chloride, magnesium chloride, mercaptoethanol, tric-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 61089 / Num. obs: 56914 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.1→20 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.101 / Num. unique all: 61089 / % possible all: 93.3 |
Reflection | *PLUS Num. obs: 61089 / Num. measured all: 419279 |
Reflection shell | *PLUS % possible obs: 93.3 % |
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Processing
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Refinement | Resolution: 2.1→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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Software | *PLUS Name: 'CNS' / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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