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- PDB-7prb: Crystal structure of Burkholderia pseudomallei heparanase in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7prb | ||||||||||||||||||||||||
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Title | Crystal structure of Burkholderia pseudomallei heparanase in complex with covalent inhibitor GR109 | ||||||||||||||||||||||||
![]() | Glyco_hydro_44 domain-containing protein | ||||||||||||||||||||||||
![]() | HYDROLASE / glycoside hydrolase / carbohydrate / glucuronidase / GH79 | ||||||||||||||||||||||||
Function / homology | Glycoside hydrolase, family 44 / Glycoside hydrolase family 44 / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / Glycoside hydrolase family 44 domain-containing protein![]() | ||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||
![]() | Wu, L. / Armstrong, Z. / Davies, G.J. | ||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism-based heparanase inhibitors reduce cancer metastasis in vivo. Authors: de Boer, C. / Armstrong, Z. / Lit, V.A.J. / Barash, U. / Ruijgrok, G. / Boyango, I. / Weitzenberg, M.M. / Schroder, S.P. / Sarris, A.J.C. / Meeuwenoord, N.J. / Bule, P. / Kayal, Y. / Ilan, N. ...Authors: de Boer, C. / Armstrong, Z. / Lit, V.A.J. / Barash, U. / Ruijgrok, G. / Boyango, I. / Weitzenberg, M.M. / Schroder, S.P. / Sarris, A.J.C. / Meeuwenoord, N.J. / Bule, P. / Kayal, Y. / Ilan, N. / Codee, J.D.C. / Vlodavsky, I. / Overkleeft, H.S. / Davies, G.J. / Wu, L. | ||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 349.4 KB | Display | ![]() |
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PDB format | ![]() | 274.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 42.2 KB | Display | |
Data in CIF | ![]() | 66.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pr6C ![]() 7pr7C ![]() 7pr8C ![]() 7pr9C ![]() 7prtC ![]() 7pshC ![]() 7psiC ![]() 7psjC ![]() 7pskC ![]() 5bwiS C: citing same article ( S: Starting model for refinement |
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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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 10 - 445 / Label seq-ID: 2 - 437
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
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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.) ![]() Strain: K96243 / Gene: BPSL2070 / Production host: ![]() ![]() #2: Polysaccharide | Type: oligosaccharide / Mass: 491.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #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: 2.61 Å3/Da / Density % sol: 52.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / 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: 1.31→66.06 Å / Num. obs: 220199 / % possible obs: 98.5 % / Redundancy: 8.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.018 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.31→1.34 Å / Rmerge(I) obs: 1.493 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 15818 / CC1/2: 0.682 / Rpim(I) all: 0.534 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5bwi Resolution: 1.31→66.06 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.983 / SU ML: 0.039 / Cross valid method: FREE R-VALUE / ESU R: 0.046 / ESU R Free: 0.047 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: 22.799 Å2
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Refinement step | Cycle: LAST / Resolution: 1.31→66.06 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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