[English] 日本語
Yorodumi- PDB-2v6y: Structure of the MIT domain from a S. solfataricus Vps4-like ATPase -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v6y | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the MIT domain from a S. solfataricus Vps4-like ATPase | ||||||
Components | (AAA FAMILY ATPASE, P60 KATANIN) x 2 | ||||||
Keywords | HYDROLASE / MIT / VPS4 / ARCHAEA / AAA-ATPASE / ATP-BINDING / MICROTUBULE INTERACTING AND TRAFFICKING DOMAIN / NUCLEOTIDE-BINDING | ||||||
Function / homology | Function and homology information | ||||||
Biological species | SULFOLOBUS SOLFATARICUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Obita, T. / Saksena, S. / Ghazi-Tabatabai, S. / Gill, D.J. / Perisic, O. / Emr, S.D. / Williams, R.L. | ||||||
Citation | Journal: Nature / Year: 2007 Title: Structural Basis for Selective Recognition of Escrt-III by the Aaa ATPase Vps4 Authors: Obita, T. / Saksena, S. / Ghazi-Tabatabai, S. / Gill, D.J. / Perisic, O. / Emr, S.D. / Williams, R.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2v6y.cif.gz | 38.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2v6y.ent.gz | 30.7 KB | Display | PDB format |
PDBx/mmJSON format | 2v6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/2v6y ftp://data.pdbj.org/pub/pdb/validation_reports/v6/2v6y | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.003859, 0.061003, 0.99813), Vector: |
-Components
#1: Protein | Mass: 9363.847 Da / Num. of mol.: 1 / Fragment: MIT DOMAIN, RESIDUES 1-83 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: POPTH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q97ZJ7, vesicle-fusing ATPase | ||||
---|---|---|---|---|---|
#2: Protein | Mass: 9349.820 Da / Num. of mol.: 1 / Fragment: MIT DOMAIN, RESIDUES 1-83 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: POPTH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q97ZJ7, vesicle-fusing ATPase | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | SSO0909 MIT DOMAIN | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.8 % / Description: NONE |
---|---|
Crystal grow | pH: 8 Details: RESERVOIR: 0.6 M AMMONIUM TARTRATE AND 2% PEG4K PROTEIN SOLUTION: 9 MG/ML IN 20 MM TRIS PH 8, 100 MM NACL, 2MM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9184 |
Detector | Type: ADSC CCD / Detector: CCD / Details: TORROIDAL MIRROR |
Radiation | Monochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→61.5 Å / Num. obs: 27901 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.9 / % possible all: 99 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 2.4→61.66 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.901 / SU B: 18.134 / SU ML: 0.198 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.33 / ESU R Free: 0.248 Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.46 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→61.66 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|