+Open data
-Basic information
Entry | Database: PDB / ID: 6q3q | ||||||
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Title | Arabidopsis OM64 TPR domain | ||||||
Components |
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Keywords | PLANT PROTEIN / Tetratrico-peptide-repeat / Mitochondria / protein import / Arabodopsis thaliana | ||||||
Function / homology | Function and homology information plant-type cell wall / protein import into mitochondrial matrix / apoplast / plant-type vacuole / protein targeting to mitochondrion / plastid / chloroplast stroma / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding ...plant-type cell wall / protein import into mitochondrial matrix / apoplast / plant-type vacuole / protein targeting to mitochondrion / plastid / chloroplast stroma / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / mitochondrial outer membrane / protein stabilization / mRNA binding / perinuclear region of cytoplasm / Golgi apparatus / ATP hydrolysis activity / protein-containing complex / mitochondrion / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Schwenkert, S. | ||||||
Citation | Journal: Mitochondrion / Year: 2019 Title: Phosphorylation of the outer membrane mitochondrial protein OM64 influences protein import into mitochondria. Authors: Nickel, C. / Horneff, R. / Heermann, R. / Neumann, B. / Jung, K. / Soll, J. / Schwenkert, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q3q.cif.gz | 83.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q3q.ent.gz | 65.6 KB | Display | PDB format |
PDBx/mmJSON format | 6q3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/6q3q ftp://data.pdbj.org/pub/pdb/validation_reports/q3/6q3q | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 13831.952 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis (plant) / Gene: OM64, TOC64-V, At5g09420, T5E8.220 / Production host: Escherichia coli (E. coli) / References: UniProt: F4KCL7 #2: Protein/peptide | Mass: 894.967 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: O03986*PLUS #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.10 M Bis-Tris pH 6.20, 0.10 M Na-Chloride, 1.10 M (NH4)2-Sulfate, 0.05 M Mg-Chloride, 0.1 M Na-Acetate, pH 4.60, 2 M (NH4)2-Sulfate |
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-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 1.54179 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 24, 2015 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2→20 Å / Num. obs: 40693 / % possible obs: 99.9 % / Redundancy: 10 % / CC1/2: 0.994 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.051 / Rrim(I) all: 0.162 / Net I/σ(I): 11.7 / Num. measured all: 407295 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.419 / SU ML: 0.065 / SU R Cruickshank DPI: 0.0919 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.095 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 157.08 Å2 / Biso mean: 33.854 Å2 / Biso min: 12.16 Å2
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Refinement step | Cycle: final / Resolution: 2→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 8528 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2→2.051 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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