[English] 日本語
![](img/lk-miru.gif)
- PDB-1jva: CRYSTAL STRUCTURE OF THE VMA1-DERIVED ENDONUCLEASE BEARING THE N ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1jva | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE VMA1-DERIVED ENDONUCLEASE BEARING THE N AND C EXTEIN PROPEPTIDES | ||||||
![]() | VMA1-DERIVED HOMING ENDONUCLEASE X10SSS | ||||||
![]() | HYDROLASE / PROTEIN-SPLICING / VMA1-DERIVED ENDONUCLEASE / INTEIN / THIAZOLIDINE INTERMEDIATE / VDE | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Mizutani, R. / Satow, Y. | ||||||
![]() | ![]() 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. #1: ![]() Title: Molecular structure of a gene, VMA1, encoding the catalytic subunit of H(+)-translocating adenosine triphosphatase from vacuolar membranes of Saccharomyces cerevisiae Authors: Hirata, R. / Ohsumi, Y. / Nakano, A. / Kawasaki, H. / Suzuki, K. / Anraku, Y. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 179.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 143.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 375.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 393.1 KB | Display | |
Data in XML | ![]() | 19.4 KB | Display | |
Data in CIF | ![]() | 30.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1vdeS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | VDE exists as a monomer in solution. |
-
Components
#1: Protein | Mass: 53150.145 Da / Num. of mol.: 2 / Fragment: RESIDUES 274-747 / Mutation: C284S/H362N/N737S/C738S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: VMA1 / Plasmid: pET-17b-VDE-X10SSS / Species (production host): Escherichia coli / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.4 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: PEG6000, BisTrisHCl, mercaptoethanol, magnesium chloride, cadmium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 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: 2.1→30 Å / Num. all: 57103 / Num. obs: 51056 / % possible obs: 89.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.5 / Redundancy: 2.39 % / Biso Wilson estimate: 20.12 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 30.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 1.63 % / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 2.63 / Num. unique all: 5699 / % possible all: 70.9 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 122186 / Rmerge(I) obs: 0.032 |
Reflection shell | *PLUS % possible obs: 70.9 % / Num. unique obs: 4038 / Rmerge(I) obs: 0.155 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1VDE Resolution: 2.1→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.3 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.18 Å / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / Rfactor all: 0.2 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.198 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.2996 / Rfactor Rwork: 0.2474 |