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Yorodumi- PDB-3ff5: Crystal structure of the conserved N-terminal domain of the perox... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ff5 | ||||||
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Title | Crystal structure of the conserved N-terminal domain of the peroxisomal matrix-protein-import receptor, Pex14p | ||||||
Components | Peroxisomal biogenesis factor 14 | ||||||
Keywords | PROTEIN TRANSPORT / protein import / peroxin / 3 helices bundle | ||||||
Function / homology | Function and homology information Class I peroxisomal membrane protein import / peroxisome transport along microtubule / E3 ubiquitin ligases ubiquitinate target proteins / protein import into peroxisome matrix, substrate release / protein import into peroxisome matrix, translocation / peroxisomal importomer complex / Peroxisomal protein import / microtubule anchoring / protein import into peroxisome matrix, docking / protein import into peroxisome matrix ...Class I peroxisomal membrane protein import / peroxisome transport along microtubule / E3 ubiquitin ligases ubiquitinate target proteins / protein import into peroxisome matrix, substrate release / protein import into peroxisome matrix, translocation / peroxisomal importomer complex / Peroxisomal protein import / microtubule anchoring / protein import into peroxisome matrix, docking / protein import into peroxisome matrix / peroxisome organization / : / peroxisomal membrane / beta-tubulin binding / negative regulation of protein binding / negative regulation of DNA-binding transcription factor activity / fibrillar center / peroxisome / transcription corepressor activity / microtubule binding / protein-containing complex assembly / membrane => GO:0016020 / signaling receptor binding / negative regulation of DNA-templated transcription / protein-containing complex / identical protein binding Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Su, J.-R. / Takeda, K. / Tamura, S. / Fujiki, Y. / Miki, K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Crystal structure of the conserved N-terminal domain of the peroxisomal matrix protein import receptor, Pex14p Authors: Su, J.R. / Takeda, K. / Tamura, S. / Fujiki, Y. / Miki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ff5.cif.gz | 35.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ff5.ent.gz | 25.5 KB | Display | PDB format |
PDBx/mmJSON format | 3ff5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/3ff5 ftp://data.pdbj.org/pub/pdb/validation_reports/ff/3ff5 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 6065.954 Da / Num. of mol.: 2 / Fragment: Conserved N-terminal domain, UNP residues 25-70 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pex14 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: Q642G4 #2: Chemical | ChemComp-DPW / | #3: 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 | Density Matthews: 2.55 Å3/Da / Density % sol: 51.79 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.2M sodium citrate, 100mM HEPES(pH7.5), 10%(v/v) glycerol, 0.2%(w/v) n-decylphosphocholine, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2008 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 11491 / Num. obs: 11491 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.8 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 39.6 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 6.3 / Num. unique all: 1799 / Rsym value: 0.361 / % possible all: 93.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.452 / SU ML: 0.078 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.132 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 17.296 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.809→1.855 Å / Total num. of bins used: 20
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