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Yorodumi- PDB-1um2: Crystal Structure of the Vma1-Derived Endonuclease with the Ligat... -
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-Basic information
Entry | Database: PDB / ID: 1um2 | ||||||
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Title | Crystal Structure of the Vma1-Derived Endonuclease with the Ligated Extein Segment | ||||||
Components |
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Keywords | HYDROLASE / Protein splicing / Vma1-derived endonuclease / VDE / intein / extein / thiazolidine | ||||||
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 / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar proton-transporting V-type ATPase complex / 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 / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar proton-transporting V-type ATPase complex / proton-transporting V-type ATPase complex / vacuolar acidification / intein-mediated protein splicing / intron homing / fungal-type vacuole membrane / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / 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 / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Mizutani, R. / Anraku, Y. / Satow, Y. | ||||||
Citation | Journal: J.Synchrotron Radiat. / Year: 2004 Title: Protein splicing of yeast VMA1-derived endonuclease via thiazolidine intermediates. Authors: Mizutani, R. / Anraku, Y. / Satow, Y. #1: Journal: J.Mol.Biol. / Year: 2002 Title: Protein-splicing reaction via a thiazolidine intermediate: crystal structure of the VMA1-derived endonuclease bearing the N and C-terminal propeptides Authors: Mizutani, R. / Nogami, S. / Kawasaki, M. / Ohya, Y. / Anraku, Y. / Satow, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1um2.cif.gz | 178.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1um2.ent.gz | 142.1 KB | Display | PDB format |
PDBx/mmJSON format | 1um2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1um2_validation.pdf.gz | 396.8 KB | Display | wwPDB validaton report |
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Full document | 1um2_full_validation.pdf.gz | 456.5 KB | Display | |
Data in XML | 1um2_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | 1um2_validation.cif.gz | 38.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/1um2 ftp://data.pdbj.org/pub/pdb/validation_reports/um/1um2 | HTTPS FTP |
-Related structure data
Related structure data | 1jvaS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 50963.789 Da / Num. of mol.: 2 / Mutation: C284S, H362N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: vma1 / Plasmid: pET-17b-VDE-X10SNS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P17255, H+-transporting two-sector ATPase #2: Protein/peptide | Mass: 2231.400 Da / Num. of mol.: 2 / Mutation: C738S Source method: isolated from a genetically manipulated source Details: The N-extein segments: residues 273-283 and C-extein segments: 738-747 were ligated by protein splicing. residue 283 links with residue 738 Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: vma1 / Plasmid: pET-17b-VDE-X10SNS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P17255, H+-transporting two-sector ATPase #3: 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: 2.44 Å3/Da / Density % sol: 49.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: PEG 6000, BistrisHCl, 2-mercaptoethanol, magnesium chloride, cadmium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.7 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 17, 2000 Details: DOUBLE CRYSTAL MONOCHROMATOR AND BENT-CYLINDER MIRROR |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. all: 20700 / Num. obs: 20700 / % possible obs: 83 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.051 |
Reflection shell | Resolution: 2.9→3 Å / Rmerge(I) obs: 0.141 / Num. unique all: 1519 / % possible all: 60.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1jva Resolution: 2.9→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.34 Å / Luzzati d res low obs: 5 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→30 Å
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Refine LS restraints |
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