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Yorodumi- PDB-7pr9: Crystal structure of Burkholderia pseudomallei heparanase in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pr9 | ||||||||||||||||||||||||
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Title | Crystal structure of Burkholderia pseudomallei heparanase in complex with covalent inhibitor VL166 | ||||||||||||||||||||||||
Components | Glyco_hydro_44 domain-containing protein | ||||||||||||||||||||||||
Keywords | 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 Function and homology information | ||||||||||||||||||||||||
Biological species | Burkholderia pseudomallei (bacteria) | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å | ||||||||||||||||||||||||
Authors | Wu, L. / Armstrong, Z. / Davies, G.J. | ||||||||||||||||||||||||
Funding support | United Kingdom, 7items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pr9.cif.gz | 348.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pr9.ent.gz | 273.9 KB | Display | PDB format |
PDBx/mmJSON format | 7pr9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pr9_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7pr9_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7pr9_validation.xml.gz | 42.3 KB | Display | |
Data in CIF | 7pr9_validation.cif.gz | 66.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/7pr9 ftp://data.pdbj.org/pub/pdb/validation_reports/pr/7pr9 | HTTPS FTP |
-Related structure data
Related structure data | 7pr6C 7pr7C 7pr8C 7prbC 7prtC 7pshC 7psiC 7psjC 7pskC 5bwiS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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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: ALA / End label comp-ID: ALA / Auth seq-ID: 10 - 446 / Label seq-ID: 2 - 438
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
#1: Protein | Mass: 44638.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (strain K96243) (bacteria) Strain: K96243 / Gene: BPSL2070 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63T97 #2: Polysaccharide | Type: oligosaccharide / Mass: 411.359 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.72 % |
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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: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 3, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→79.89 Å / Num. obs: 210296 / % possible obs: 98.9 % / Redundancy: 7.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.022 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.34→1.37 Å / Rmerge(I) obs: 1.215 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 14341 / CC1/2: 0.565 / Rpim(I) all: 0.607 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5bwi Resolution: 1.34→77.002 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.045 / SU ML: 0.041 / Cross valid method: FREE R-VALUE / ESU R: 0.051 / ESU R Free: 0.053 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: 21.494 Å2
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Refinement step | Cycle: LAST / Resolution: 1.34→77.002 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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