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- PDB-5mc3: Crystal Structure of Glu412Lys mutant of Human Prolidase with Mn ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5mc3 | ||||||
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Title | Crystal Structure of Glu412Lys mutant of Human Prolidase with Mn ions and GlyPro ligand | ||||||
![]() | Xaa-Pro dipeptidase | ||||||
![]() | HYDROLASE / prolidase / peptidase / hydrolysis / pita-bread / metalloenzyme / mutation | ||||||
Function / homology | ![]() Xaa-Pro dipeptidase / proline dipeptidase activity / amino acid metabolic process / negative regulation of programmed cell death / metalloaminopeptidase activity / collagen catabolic process / metallocarboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / extracellular exosome Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Wilk, P. / Mueller, U. / Dobbek, H. / Weiss, M.S. | ||||||
![]() | ![]() Title: Structural basis for prolidase deficiency disease mechanisms. Authors: Wilk, P. / Uehlein, M. / Piwowarczyk, R. / Dobbek, H. / Mueller, U. / Weiss, M.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 432.1 KB | Display | ![]() |
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PDB format | ![]() | 353.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 479.5 KB | Display | ![]() |
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Full document | ![]() | 484 KB | Display | |
Data in XML | ![]() | 44.5 KB | Display | |
Data in CIF | ![]() | 68.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mbyC ![]() 5mbzC ![]() 5mc0C ![]() 5mc1C ![]() 5mc2C ![]() 5mc4C ![]() 5mc5C ![]() 6h2pC ![]() 6h2qC ![]() 5m4jS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 53799.160 Da / Num. of mol.: 2 / Mutation: E412K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 7 types, 959 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/GLY.gif)
![](data/chem/img/PRO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/GLY.gif)
![](data/chem/img/PRO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-GOL / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 10mM NaBorate, 690-760mM NaCitrate / PH range: 7.2-7.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 9, 2015 |
Radiation | Monochromator: Double Crystal Monochromator Si-11 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.518→47.79 Å / Num. obs: 183636 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.75 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.86 |
Reflection shell | Resolution: 1.52→1.61 Å / Redundancy: 5.56 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 1.82 / % possible all: 98.3 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5M4J Resolution: 1.52→47.79 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.52→47.79 Å
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Refine LS restraints |
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LS refinement shell |
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