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Yorodumi- PDB-5e98: Crystal structure of human heparanase in complex with HepMer M04S02a -
+Open data
-Basic information
Entry | Database: PDB / ID: 5.0E+98 | ||||||||||||
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Title | Crystal structure of human heparanase in complex with HepMer M04S02a | ||||||||||||
Components | (Heparanase) x 2 | ||||||||||||
Keywords | HYDROLASE / glycoside hydrolase / heparan / protein / sugar | ||||||||||||
Function / homology | Function and homology information heparanase / heparanase activity / regulation of hair follicle development / heparin metabolic process / beta-glucuronidase activity / heparan sulfate proteoglycan catabolic process / proteoglycan metabolic process / HS-GAG degradation / protein transmembrane transport / positive regulation of hair follicle development ...heparanase / heparanase activity / regulation of hair follicle development / heparin metabolic process / beta-glucuronidase activity / heparan sulfate proteoglycan catabolic process / proteoglycan metabolic process / HS-GAG degradation / protein transmembrane transport / positive regulation of hair follicle development / 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 / extracellular matrix / lysosomal lumen / cell-matrix adhesion / response to organic substance / specific granule lumen / lysosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / membrane raft / lysosomal membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / extracellular space / extracellular region / nucleoplasm / nucleus Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||||||||
Authors | Wu, L. / Davies, G.J. | ||||||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2015 Title: Structural characterization of human heparanase reveals insights into substrate recognition. Authors: Wu, L. / Viola, C.M. / Brzozowski, A.M. / Davies, G.J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e98.cif.gz | 207.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e98.ent.gz | 159.3 KB | Display | PDB format |
PDBx/mmJSON format | 5e98.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/5e98 ftp://data.pdbj.org/pub/pdb/validation_reports/e9/5e98 | HTTPS FTP |
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-Related structure data
Related structure data | 5e8mSC 5e97C 5e9bC 5e9cC S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 43733.324 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y251, heparanase |
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#2: Protein | Mass: 8542.769 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y251, heparanase |
-Sugars , 2 types, 4 molecules
#3: Polysaccharide | beta-D-glucopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid Source method: isolated from a genetically manipulated source |
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#5: Sugar |
-Non-polymers , 4 types, 246 molecules
#4: Chemical | ChemComp-IMD / |
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#6: Chemical | ChemComp-CL / |
#7: Chemical | ChemComp-NPO / |
#8: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M MES [5.5] 0.1 M MgCl2 17% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→38.45 Å / Num. obs: 61989 / % possible obs: 99.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.63→1.67 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.077 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4543 / CC1/2: 0.465 / Rpim(I) all: 0.625 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5e8m Resolution: 1.63→38.45 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.222 / WRfactor Rwork: 0.179 / SU B: 2.135 / SU ML: 0.07 / Average fsc free: 0.906 / Average fsc work: 0.9146 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.089 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.312 Å2
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Refinement step | Cycle: LAST / Resolution: 1.63→38.45 Å
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Refine LS restraints |
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LS refinement shell |
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