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Yorodumi- PDB-5az6: Crystal structure of MBP-Tom20 fusion protein with a 2-residue sp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5az6 | |||||||||
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Title | Crystal structure of MBP-Tom20 fusion protein with a 2-residue spacer in the connector helix | |||||||||
Components | Maltose-binding periplasmic protein,Mitochondrial import receptor subunit TOM20 homolog | |||||||||
Keywords | SUGAR BINDING PROTEIN / PEPTIDE BINDING PROTEIN / Fusion protein | |||||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å | |||||||||
Authors | Matsuoka, R. / Kohda, D. | |||||||||
Citation | Journal: Protein Sci. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5az6.cif.gz | 179.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5az6.ent.gz | 142.2 KB | Display | PDB format |
PDBx/mmJSON format | 5az6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5az6_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5az6_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5az6_validation.xml.gz | 32.9 KB | Display | |
Data in CIF | 5az6_validation.cif.gz | 44.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/5az6 ftp://data.pdbj.org/pub/pdb/validation_reports/az/5az6 | HTTPS FTP |
-Related structure data
Related structure data | 5az7C 5az8C 5az9C 5azaC 1anfS 2v1tS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-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.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Rattus norvegicus (Norway rat) Strain: K12 / Gene: malE, b4034, JW3994, Tomm20 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: Q62760 #2: Polysaccharide | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.67 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
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
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
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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: 60.183 Å2
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Refinement step | Cycle: LAST / Resolution: 2.56→24.72 Å
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