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Open data
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Basic information
Entry | Database: PDB / ID: 7z0j | ||||||
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Title | human PEX13 SH3 domain in complex with internal FxxxF motif | ||||||
![]() | Peroxisomal membrane protein PEX13 | ||||||
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Function / homology | ![]() microtubule-based peroxisome localization / protein import into peroxisome matrix, translocation / peroxisomal importomer complex / protein import into peroxisome matrix, docking / Class I peroxisomal membrane protein import / fatty acid alpha-oxidation / peroxisomal membrane / suckling behavior / cerebral cortex cell migration / protein transmembrane transporter activity ...microtubule-based peroxisome localization / protein import into peroxisome matrix, translocation / peroxisomal importomer complex / protein import into peroxisome matrix, docking / Class I peroxisomal membrane protein import / fatty acid alpha-oxidation / peroxisomal membrane / suckling behavior / cerebral cortex cell migration / protein transmembrane transporter activity / locomotory behavior / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gaussmann, S. / Zak, K. / Kreisz, N. / Sattler, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Intramolecular autoinhibition of human PEX13 modulates peroxisomal import Authors: Gaussmann, S. / Ott, J. / Zak, K.M. / Delhommel, F. / Popowicz, G.M. / Schliebs, W. / Erdmann, R. / Sattler, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.5 KB | Display | ![]() |
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PDB format | ![]() | 33.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7z0iSC ![]() 7z0kC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0
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Components
#1: Protein | Mass: 11573.688 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ![]() #3: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 60 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M Sodium chloride 0.1 M Bis-Tris pH 6.5 25% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 24, 2020 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||
Reflection | Resolution: 2.3→49.41 Å / Num. obs: 12998 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.997 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.091 / Rrim(I) all: 0.296 / Net I/σ(I): 11.8 | |||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 7Z0I Resolution: 2.3→49.41 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.496 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.21 Å2 / Biso mean: 42.331 Å2 / Biso min: 24.16 Å2
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Refinement step | Cycle: final / Resolution: 2.3→49.41 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 2238 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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