[English] 日本語
![](img/lk-miru.gif)
- PDB-5az6: Crystal structure of MBP-Tom20 fusion protein with a 2-residue sp... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5az6 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of MBP-Tom20 fusion protein with a 2-residue spacer in the connector helix | |||||||||
![]() | Maltose-binding periplasmic protein,Mitochondrial import receptor subunit TOM20 homolog | |||||||||
![]() | SUGAR BINDING PROTEIN / PEPTIDE BINDING PROTEIN / Fusion protein | |||||||||
Function / homology | ![]() tRNA import into mitochondrion / PINK1-PRKN Mediated Mitophagy / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / response to 3,3',5-triiodo-L-thyronine / migrasome / mitochondria-associated endoplasmic reticulum membrane contact site / Ub-specific processing proteases / protein import into mitochondrial matrix / protein-transporting ATPase activity ...tRNA import into mitochondrion / PINK1-PRKN Mediated Mitophagy / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / response to 3,3',5-triiodo-L-thyronine / migrasome / mitochondria-associated endoplasmic reticulum membrane contact site / Ub-specific processing proteases / protein import into mitochondrial matrix / protein-transporting ATPase activity / protein targeting to mitochondrion / mitochondrial envelope / response to muscle activity / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / sperm midpiece / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / cell periphery / intracellular protein transport / unfolded protein binding / outer membrane-bounded periplasmic space / mitochondrial outer membrane / periplasmic space / DNA damage response / mitochondrion / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Matsuoka, R. / Kohda, D. | |||||||||
![]() | ![]() Title: Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules. Authors: Matsuoka, R. / Shimada, A. / Komuro, Y. / Sugita, Y. / Kohda, D. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 179.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 142.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 32.9 KB | Display | |
Data in CIF | ![]() | 44.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5az7C ![]() 5az8C ![]() 5az9C ![]() 5azaC ![]() 1anfS ![]() 2v1tS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 47860.379 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 27-394,UNP RESIDUES 65-126 / Mutation: A313V Source method: isolated from a genetically manipulated source Details: The fusion protein of 1-369 Maltose binding protein, 370-371 Linker, and 372-433 Tom20 Source: (gene. exp.) ![]() ![]() ![]() ![]() Strain: K12 / Gene: malE, b4034, JW3994, Tomm20 / Production host: ![]() ![]() #2: Polysaccharide | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.67 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 16% PEG 3350, 0.2M Disodium malonate, 0.1M HEPES (pH7.3) |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 24, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→50 Å / Num. obs: 35889 / % possible obs: 99.9 % / Redundancy: 3.79 % / Net I/σ(I): 11 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1ANF, 2V1T Resolution: 2.56→24.72 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.92 / SU B: 13.48 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R: 0.531 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 60.183 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.56→24.72 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|