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Yorodumi- PDB-2zxt: Crystal structure of Tim40/MIA40, a disulfide relay system in mit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zxt | |||||||||
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Title | Crystal structure of Tim40/MIA40, a disulfide relay system in mitochondria, solved as MBP fusion protein | |||||||||
Components | Maltose-binding periplasmic protein, LINKER, Mitochondrial intermembrane space import and assembly protein 40 | |||||||||
Keywords | PROTEIN TRANSPORT / disulfide bond / alpha helix / fusion / Sugar transport / Transport / Membrane / Mitochondrion / Mitochondrion inner membrane / Phosphoprotein / Signal-anchor / Transit peptide / Translocation / Transmembrane | |||||||||
Function / homology | Function and homology information thiol oxidase activity / protein import into mitochondrial intermembrane space / protein maturation by protein folding / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / protein disulfide isomerase activity / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity ...thiol oxidase activity / protein import into mitochondrial intermembrane space / protein maturation by protein folding / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / protein disulfide isomerase activity / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / protein-disulfide reductase activity / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / protein folding / outer membrane-bounded periplasmic space / mitochondrial inner membrane / periplasmic space / oxidoreductase activity / DNA damage response / mitochondrion / membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) synthetic construct (others) Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Kawano, S. / Momose, T. / Watanabe, N. / Endo, T. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Structural basis of yeast Tim40/Mia40 as an oxidative translocator in the mitochondrial intermembrane space. Authors: Kawano, S. / Yamano, K. / Naoe, M. / Momose, T. / Terao, K. / Nishikawa, S. / Watanabe, N. / Endo, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zxt.cif.gz | 100.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zxt.ent.gz | 75.2 KB | Display | PDB format |
PDBx/mmJSON format | 2zxt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/2zxt ftp://data.pdbj.org/pub/pdb/validation_reports/zx/2zxt | HTTPS FTP |
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-Related structure data
Related structure data | 3a3cC 1anfS 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
#1: Protein | Mass: 51362.598 Da / Num. of mol.: 1 / Fragment: MBPTim40C4 Source method: isolated from a genetically manipulated source Details: THE FUSION PROTEIN OF MMBP (UNP RESIDUES 27-392), LINKER (NSSSVPGRGSIEGRPEF), MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE TIM40 (UNP RESIDUES 284-365) Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) synthetic construct (others), (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: MIA40, TIM40, YKL195W / Organelle: mitochondriaMitochondrion / Plasmid: pMal-c2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P0AEX9, UniProt: P36046 |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
#3: Water | ChemComp-HOH / |
Sequence details | THE FUSION PROTEIN OF MMBP (UNP RESIDUES 27-392), LINKER (NSSSVPGRGSIEGRPEF), MITOCHONDRIAL IMPORT ...THE FUSION PROTEIN OF MMBP (UNP RESIDUES 27-392), LINKER (NSSSVPGRGS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 100mM KOAc, 200 mM NH4OAc, 30 % PEG 4000, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Sep 25, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3→90 Å / Num. obs: 9692 / % possible obs: 99.6 % / Redundancy: 12.6 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 22.2 / Num. unique all: 943 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ANF Resolution: 3→31.33 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.87 / SU B: 50.493 / SU ML: 0.429 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.529 / 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: 8.356 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→31.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.004→3.081 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -18.188 Å / Origin y: -2.061 Å / Origin z: -19.094 Å
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Xplor file |
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