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- PDB-6gci: Structure of the bongkrekic acid-inhibited mitochondrial ADP/ATP ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gci | ||||||||||||
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Title | Structure of the bongkrekic acid-inhibited mitochondrial ADP/ATP carrier | ||||||||||||
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![]() | MEMBRANE PROTEIN / Transporter / Inhibitor / Mitochondrial / Carrier | ||||||||||||
Function / homology | ![]() ATP:ADP antiporter activity / mitochondrial ADP transmembrane transport / mitochondrial ATP transmembrane transport / mitochondrial inner membrane / membrane => GO:0016020 Similarity search - Function | ||||||||||||
Biological species | Thermothelomyces thermophila![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Ruprecht, J.J. / King, M.S. / Pardon, E. / Aleksandrova, A.A. / Zogg, T. / Crichton, P.G. / Steyaert, J. / Kunji, E.R.S. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: The Molecular Mechanism of Transport by the Mitochondrial ADP/ATP Carrier. Authors: Ruprecht, J.J. / King, M.S. / Zogg, T. / Aleksandrova, A.A. / Pardon, E. / Crichton, P.G. / Steyaert, J. / Kunji, E.R.S. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 189.4 KB | Display | ![]() |
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PDB format | ![]() | 147.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 23.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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 on special symmetry positions |
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Components
#1: Protein | Mass: 34042.578 Da / Num. of mol.: 1 / Mutation: Q302K Source method: isolated from a genetically manipulated source Details: Sequence has Q302K mutation Source: (gene. exp.) ![]() Strain: ATCC 42464 / BCRC 31852 / DSM 1799 / Gene: MYCTH_2316753 / Plasmid: pYES3 / Details (production host): modified / Production host: ![]() ![]() | ||
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#2: Antibody | Mass: 14521.907 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Nanobody selected against the BKA-inhibited ADP/ATP carrier Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#3: Chemical | ChemComp-BKC / | ||
#4: Chemical | ChemComp-CDL / #5: Chemical | ChemComp-P6G / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.03 Å3/Da / Density % sol: 75.53 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop Details: 0.1M MES pH 6.5, 1% 3-methyl-3-pentanol, 22% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→29.35 Å / Num. obs: 13204 / % possible obs: 85.1 % / Redundancy: 4.7 % / Biso Wilson estimate: 111.32 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 3.3→3.43 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 659 / % possible all: 40.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5IMK, 4C9H Resolution: 3.3→29.35 Å / Cor.coef. Fo:Fc: 0.869 / Cor.coef. Fo:Fc free: 0.889 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.484 / SU Rfree Cruickshank DPI: 0.487 Details: (A) Crystal diffracted anisotropically, and data was treated with STARANISO. (B) Fourier map coefficients have been deposited along with the observed data. (C) A PEG molecule lies on a ...Details: (A) Crystal diffracted anisotropically, and data was treated with STARANISO. (B) Fourier map coefficients have been deposited along with the observed data. (C) A PEG molecule lies on a symmetry axis (special position) and has been modelled with occupancy=0.5. (D) Some cardiolipins molecules have been modelled with partial occupancy, as described in the accompanying paper. (E) Met250-Ser252 and Lys257 lie in very weak electron density. Their position is supported by good electron density obtained from an earlier crystal. (F) There are unmodelled bits of electron density near the N-terminus of the carrier, which are likely to be lipid headgroups/tails. (G) Additional electron density at the C-terminus of the carrier indicates where the C-terminal tail is likely to run, but it is not possible to model this accurately. (H) The structure factor file contains a second data block containing the structure factors from a crystal of BKA-inhibited TtAac grown without the nanobody. This P212121 crystal diffracted to lower resolution and with significant anisotropy, but was used to confirm the domain positions observed in the P3221 crystal of the TtAac-Nb complex. Full details can be found in the primary citation.
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Displacement parameters | Biso mean: 111.34 Å2
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Refine analyze | Luzzati coordinate error obs: 0.55 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.3→29.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.57 Å / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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