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- PDB-5l9z: Crystal structure of human heparanase nucleophile mutant (E343Q),... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5l9z | |||||||||||||||
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Title | Crystal structure of human heparanase nucleophile mutant (E343Q), in complex with unreacted glucuronic acid configured aziridine probe JJB355 | |||||||||||||||
![]() | (Heparanase) x 2 | |||||||||||||||
![]() | HYDROLASE / Heparanase / Probe / GH79 | |||||||||||||||
Function / homology | ![]() heparanase / heparanase activity / regulation of hair follicle development / heparin metabolic process / proteoglycan metabolic process / heparan sulfate proteoglycan catabolic process / beta-glucuronidase activity / positive regulation of hair follicle development / HS-GAG degradation / protein transmembrane transport ...heparanase / heparanase activity / regulation of hair follicle development / heparin metabolic process / proteoglycan metabolic process / heparan sulfate proteoglycan catabolic process / beta-glucuronidase activity / positive regulation of hair follicle development / HS-GAG degradation / protein transmembrane transport / syndecan binding / vascular wound healing / angiogenesis involved in wound healing / establishment of endothelial barrier / positive regulation of osteoblast proliferation / positive regulation of vascular endothelial growth factor production / positive regulation of blood coagulation / lysosomal lumen / cell-matrix adhesion / : / extracellular matrix / specific granule lumen / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lysosome / membrane raft / lysosomal membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / extracellular space / extracellular region / nucleoplasm / nucleus Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Wu, L. / Jin, Y. / Davies, G.J. | |||||||||||||||
Funding support | ![]() ![]() ![]()
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![]() | ![]() Title: Activity-based probes for functional interrogation of retaining beta-glucuronidases. Authors: Wu, L. / Jiang, J. / Jin, Y. / Kallemeijn, W.W. / Kuo, C.L. / Artola, M. / Dai, W. / van Elk, C. / van Eijk, M. / van der Marel, G.A. / Codee, J.D.C. / Florea, B.I. / Aerts, J.M.F.G. / ...Authors: Wu, L. / Jiang, J. / Jin, Y. / Kallemeijn, W.W. / Kuo, C.L. / Artola, M. / Dai, W. / van Elk, C. / van Eijk, M. / van der Marel, G.A. / Codee, J.D.C. / Florea, B.I. / Aerts, J.M.F.G. / Overkleeft, H.S. / Davies, G.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 | ![]() | 122.3 KB | Display | ![]() |
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PDB format | ![]() | 91.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 721.5 KB | Display | ![]() |
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Full document | ![]() | 724.4 KB | Display | |
Data in XML | ![]() | 23.9 KB | Display | |
Data in CIF | ![]() | 35.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5g0qC ![]() 5l77C ![]() 5l9yC ![]() 5la4C ![]() 5la7C ![]() 5e8mS 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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1 |
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 43732.340 Da / Num. of mol.: 1 / Fragment: UNP residues 158-543 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 8542.769 Da / Num. of mol.: 1 / Fragment: UNP residues 36-109 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Sugars , 1 types, 4 molecules ![](data/chem/img/NAG.gif)
#3: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 413 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GUX.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GUX.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | ChemComp-GUX / ( | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 17% PEG3350 0.1 M MES 5.5 0.1 M MgCl2 200 nL:500 nL protein:drop ratio |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→46 Å / Num. obs: 70155 / % possible obs: 99.2 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.57→1.61 Å / Redundancy: 4 % / Rmerge(I) obs: 0.862 / Mean I/σ(I) obs: 1.7 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5E8M Resolution: 1.57→46 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.881 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 29.93 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→46 Å
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Refine LS restraints |
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