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- PDB-8ohw: Crystal structure of heparanase from Burkholderia pseudomallei in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ohw | |||||||||||||||||||||
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Title | Crystal structure of heparanase from Burkholderia pseudomallei in complex with siastatin B derived inhibitor | |||||||||||||||||||||
![]() | Glycoside hydrolase family 44 domain-containing protein | |||||||||||||||||||||
![]() | HYDROLASE / Inhibitor / Complex | |||||||||||||||||||||
Function / homology | Glycoside hydrolase, family 44 / Glycoside hydrolase family 44 / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / Chem-VON / Glycoside hydrolase family 44 domain-containing protein![]() | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Armstrong, Z. / Yurong, C. / Wu, L. / Overkleeft, H.S. / Davies, G.J. | |||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Molecular Basis for Inhibition of Heparanases and beta-Glucuronidases by Siastatin B. Authors: Chen, Y. / van den Nieuwendijk, A.M.C.H. / Wu, L. / Moran, E. / Skoulikopoulou, F. / van Riet, V. / Overkleeft, H.S. / Davies, G.J. / Armstrong, Z. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.6 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8cqiC ![]() 8ogxC ![]() 8ohqC ![]() 8ohrC ![]() 8ohtC ![]() 8ohuC ![]() 8ohvC ![]() 8ohxC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44638.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium citrate pH 5.0, 14% (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 30, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 1.27→61.758 Å / Num. obs: 238876 / % possible obs: 99.9 % / Redundancy: 8.2 % / CC1/2: 0.999 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.27→1.29 Å / Num. unique obs: 11543 / CC1/2: 0.518 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 17.891 Å2
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Refinement step | Cycle: LAST / Resolution: 1.27→61.758 Å
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Refine LS restraints |
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LS refinement shell |
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