+Open data
-Basic information
Entry | Database: PDB / ID: 5yfb | ||||||
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Title | Crystal structure of a new DPP III family member | ||||||
Components | Dipeptidyl peptidase 3 | ||||||
Keywords | HYDROLASE / dipeptidyl peptidase III / aflatoxin-oxidase | ||||||
Function / homology | Function and homology information dipeptidyl-peptidase III / metalloexopeptidase activity / dipeptidyl-peptidase activity / aminopeptidase activity / proteolysis / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Armillaria tabescens (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Xu, T. / Sun, Z. / Liu, J. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2017 Title: Crystal structures of Aflatoxin-oxidase from Armillariella tabescens reveal a dual activity enzyme. Authors: Xu, T. / Xie, C. / Yao, D. / Zhou, C.Z. / Liu, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yfb.cif.gz | 281.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yfb.ent.gz | 226.4 KB | Display | PDB format |
PDBx/mmJSON format | 5yfb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yfb_validation.pdf.gz | 470.7 KB | Display | wwPDB validaton report |
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Full document | 5yfb_full_validation.pdf.gz | 483.4 KB | Display | |
Data in XML | 5yfb_validation.xml.gz | 49.4 KB | Display | |
Data in CIF | 5yfb_validation.cif.gz | 69.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/5yfb ftp://data.pdbj.org/pub/pdb/validation_reports/yf/5yfb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 78181.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Armillaria tabescens (fungus) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B0S4Q0, dipeptidyl-peptidase III #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-EDO / #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 | Density Matthews: 2.44 Å3/Da / Density % sol: 49.68 % / Mosaicity: 0.29 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 0.2 M Sodium formate pH 7.0, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 22, 2015 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.2→98.27 Å / Num. obs: 73866 / % possible obs: 98.4 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.024 / Rrim(I) all: 0.062 / Net I/σ(I): 14.6 / Num. measured all: 472137 / Scaling rejects: 904 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 6.6 %
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-Processing
Software |
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Refinement | Resolution: 2.2→98.27 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.889 / SU B: 5.895 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.28 / ESU R Free: 0.223 / 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: 88.54 Å2 / Biso mean: 24.031 Å2 / Biso min: 3.75 Å2
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Refinement step | Cycle: final / Resolution: 2.2→98.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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