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Yorodumi- PDB-5az7: Crystal structure of MBP-Tom20 fusion protein with a 4-residue sp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5az7 | |||||||||
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Title | Crystal structure of MBP-Tom20 fusion protein with a 4-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: 1.96 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 | 5az7.cif.gz | 101 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5az7.ent.gz | 75 KB | Display | PDB format |
PDBx/mmJSON format | 5az7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5az7_validation.pdf.gz | 840.4 KB | Display | wwPDB validaton report |
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Full document | 5az7_full_validation.pdf.gz | 847.8 KB | Display | |
Data in XML | 5az7_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 5az7_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/5az7 ftp://data.pdbj.org/pub/pdb/validation_reports/az/5az7 | HTTPS FTP |
-Related structure data
Related structure data | 5az6C 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 48028.551 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 27-394,UNP RESIDUES 65-126 / Mutation: A313V, C409S,A313V, C409S Source method: isolated from a genetically manipulated source Details: The fusion protein of 1-369 Maltose binding protein, 370-373 Linker and 374-435 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 |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4 / Details: 50% PEG 400, 0.1M Phosphate citrate (pH 4.4) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 24, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→50 Å / Num. obs: 30663 / % possible obs: 93.1 % / Redundancy: 6.14 % / Net I/σ(I): 14.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ANF, 2V1T Resolution: 1.96→42.22 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.497 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
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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: 35.961 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→42.22 Å
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Refine LS restraints |
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