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- PDB-5az9: Crystal structure of (5-residue deleted)MBP-Tom20 fusion protein ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5az9 | ||||||
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Title | Crystal structure of (5-residue deleted)MBP-Tom20 fusion protein tethered with ALDH presequence via a disulfide bond | ||||||
![]() | Maltose-binding periplasmic protein,Mitochondrial import receptor subunit TOM20 homolog | ||||||
![]() | SUGAR BINDING PROTEIN / PEPTIDE BINDING PROTEIN / Fusion protein Complex | ||||||
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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.6 KB | Display | ![]() |
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PDB format | ![]() | 75.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.4 KB | Display | ![]() |
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Full document | ![]() | 434 KB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 26.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5az6C ![]() 5az7C ![]() 5az8C ![]() 5azaC ![]() 1anfS ![]() 2v1tS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 47629.223 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 27-394,UNP RESIDUES 65-126 / Mutation: A308V Source method: isolated from a genetically manipulated source Details: The fusion protein of 1-364 Maltose binding protein, 365-368 Linker and 369-430 Tom20 Source: (gene. exp.) ![]() ![]() ![]() ![]() Strain: K12 / Gene: malE, b4034, JW3994, Tomm20 / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2M Potassium nitrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 23, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→50 Å / Num. obs: 46512 / % possible obs: 99.8 % / Redundancy: 3.64 % / Net I/σ(I): 14 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ANF, 2V1T Resolution: 1.82→39.55 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.129 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 36.707 Å2
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Refinement step | Cycle: LAST / Resolution: 1.82→39.55 Å
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Refine LS restraints |
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