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Yorodumi- PDB-3cvn: Structure of Peroxisomal Targeting Signal 1 (PTS1) binding domain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cvn | ||||||
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Title | Structure of Peroxisomal Targeting Signal 1 (PTS1) binding domain of Trypanosoma brucei Peroxin 5 (TbPEX5)complexed to T. brucei Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) PTS1 peptide | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / TPR motifs / TPR protein / Peroxin 5 / PEX5 / PTS1 binding domain / Protein-peptide complex / Receptor / TPR repeat | ||||||
Function / homology | Function and homology information peroxisome matrix targeting signal-1 binding / protein import into peroxisome matrix, docking / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycosome / peroxisomal membrane / glycolytic process / peroxisome / glucose metabolic process / NAD binding ...peroxisome matrix targeting signal-1 binding / protein import into peroxisome matrix, docking / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycosome / peroxisomal membrane / glycolytic process / peroxisome / glucose metabolic process / NAD binding / NADP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Sampathkumar, P. / Roach, C. / Michels, P.A.M. / Hol, W.G.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structural Insights into the recognition of peroxisomal targeting signal 1 by Trypanosoma brucei peroxin 5. Authors: Sampathkumar, P. / Roach, C. / Michels, P.A. / Hol, W.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cvn.cif.gz | 78.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cvn.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 3cvn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/3cvn ftp://data.pdbj.org/pub/pdb/validation_reports/cv/3cvn | HTTPS FTP |
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-Related structure data
Related structure data | 3cv0C 3cvlC 3cvpC 3cvqC 1fchS C: citing same article (ref.) S: Starting model for refinement |
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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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Details | THE BIOLOGICAL UNIT OF PROTEIN PEX5 IS MONOMER |
-Components
#1: Protein | Mass: 36545.844 Da / Num. of mol.: 1 / Fragment: Binding domain,UNP residues 332-655 / Mutation: K378A/E379A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: PEX5 / Plasmid details: Derivative pET28 / Plasmid: pSKB3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q57W55, UniProt: Q9U7C3*PLUS | ||
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#2: Protein/peptide | Mass: 831.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P22512 | ||
#3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 2.3M Potassium acetate, 0.1M sodium citrate monohydrate, pH 4.8 - 5.0, vapor diffusion, sitting drop, temperature 298KK PH range: 4.8 - 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 7, 2006 / Details: Osmic VariMax optics |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→43.19 Å / Num. all: 19925 / Num. obs: 19415 / % possible obs: 97.6 % / Observed criterion σ(I): 5 / Redundancy: 3.48 % / Biso Wilson estimate: 24.79 Å2 / Rsym value: 0.098 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.32 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 1538 / Rsym value: 0.316 / % possible all: 81.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB code 1FCH Resolution: 2→40.06 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.905 / SU B: 4.975 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.222 / ESU R Free: 0.203 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.734 Å2
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Refinement step | Cycle: LAST / Resolution: 2→40.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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