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Yorodumi- PDB-3a3c: Crystal structure of TIM40/MIA40 fusing MBP, C296S and C298S mutant -
+Open data
-Basic information
Entry | Database: PDB / ID: 3a3c | |||||||||
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Title | Crystal structure of TIM40/MIA40 fusing MBP, C296S and C298S mutant | |||||||||
Components | Maltose-binding periplasmic protein, LINKER, Mitochondrial intermembrane space import and assembly protein 40 | |||||||||
Keywords | PROTEIN TRANSPORT / Mitochondrion / inner membrane space / membrane / disulfide bond transfer / alpha helices / Sugar transport / Transport / 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 / protein disulfide isomerase activity / detection of maltose stimulus / maltose transport complex / carbohydrate transport / maltose binding / maltose transport / maltodextrin transmembrane transport ...thiol oxidase activity / protein import into mitochondrial intermembrane space / protein maturation by protein folding / protein disulfide isomerase activity / detection of maltose stimulus / maltose transport complex / carbohydrate transport / maltose binding / maltose transport / maltodextrin transmembrane transport / protein-disulfide reductase activity / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Kawano, S. / Naoe, M. / 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 | 3a3c.cif.gz | 103.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a3c.ent.gz | 77.3 KB | Display | PDB format |
PDBx/mmJSON format | 3a3c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3a3c_validation.pdf.gz | 838.9 KB | Display | wwPDB validaton report |
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Full document | 3a3c_full_validation.pdf.gz | 857 KB | Display | |
Data in XML | 3a3c_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 3a3c_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/3a3c ftp://data.pdbj.org/pub/pdb/validation_reports/a3/3a3c | HTTPS FTP |
-Related structure data
Related structure data | 2zxtSC S: Starting model for refinement C: citing same article (ref.) |
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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: 49713.805 Da / Num. of mol.: 1 / Mutation: C296S, C298S Source method: isolated from a genetically manipulated source Details: THE FUSION PROTEIN OF MMBP (UNP RESIDUES 29-392), LINKER (NSSSVPGRGSIEGRPEF), MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE TIM40 (UNP RESIDUES 284-353) 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 / 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 29-392), LINKER (NSSSVPGRGSIEGRPEF), MITOCHONDRIAL IMPORT ...THE FUSION PROTEIN OF MMBP (UNP RESIDUES 29-392), LINKER (NSSSVPGRGS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.23 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 100mM K-acetate, 200 mM NH4-acetate, 30% PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Detector: CCD / Date: Feb 24, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 16430 / Num. obs: 15266 / % possible obs: 91.3 % / Redundancy: 12.1 % / Biso Wilson estimate: 26.4 Å2 / Rsym value: 0.138 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 9.5 / Num. unique all: 1519 / Rsym value: 0.626 / % possible all: 91.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZXT Resolution: 2.5→30.88 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 177067.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.1652 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 41.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→30.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.053 / Total num. of bins used: 6
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Xplor file |
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