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Open data
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Basic information
Entry | Database: PDB / ID: 5yfc | ||||||
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Title | Crystal structure of a new DPP III family member | ||||||
![]() | Dipeptidyl peptidase 3 | ||||||
![]() | HYDROLASE / dipeptidyl peptidase III / aflatoxin-oxidase | ||||||
Function / homology | ![]() dipeptidyl-peptidase III / metalloexopeptidase activity / dipeptidyl-peptidase activity / aminopeptidase activity / proteolysis / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Xu, T. / Liu, J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 319.1 KB | Display | ![]() |
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PDB format | ![]() | 254.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 482 KB | Display | ![]() |
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Full document | ![]() | 500.6 KB | Display | |
Data in XML | ![]() | 64.4 KB | Display | |
Data in CIF | ![]() | 99.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 78181.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1483 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.26 % / Mosaicity: 0.25 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1 M Tris-HCl pH 8.5, 2.5 M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 22, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.76→59.01 Å / Num. obs: 134694 / % possible obs: 98 % / Redundancy: 7.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.027 / Rrim(I) all: 0.071 / Net I/σ(I): 22.6 / Num. measured all: 968571 / Scaling rejects: 5046 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Resolution: 1.76→59.01 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.954 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.113 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: 74.3 Å2 / Biso mean: 10.813 Å2 / Biso min: 2.82 Å2
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Refinement step | Cycle: final / Resolution: 1.76→59.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.764→1.81 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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