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- PDB-7psh: Crystal structure of beta-glucuronidase from Acidobacterium capsu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7psh | ||||||||||||||||||||||||
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Title | Crystal structure of beta-glucuronidase from Acidobacterium capsulatum at 1.24 Angstrom resolution | ||||||||||||||||||||||||
![]() | Beta-glucuronidase | ||||||||||||||||||||||||
![]() | CARBOHYDRATE / glycoside hydrolase / glucuronidase / GH79 / heparan sulfate | ||||||||||||||||||||||||
Function / homology | Beta-glucuronidase, C-terminal / Glycosyl hydrolase family 79 C-terminal beta domain / Glycoside hydrolase, family 79 / Glycosyl hydrolase family 79, N-terminal domain / hydrolase activity, acting on glycosyl bonds / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / membrane / Beta-glucuronidase C-terminal domain-containing protein![]() | ||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||
![]() | Armstrong, Z. / Wu, L. / 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 | ![]() | 111.1 KB | Display | ![]() |
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PDB format | ![]() | 80.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.5 KB | Display | ![]() |
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Full document | ![]() | 426.1 KB | Display | |
Data in XML | ![]() | 21.1 KB | Display | |
Data in CIF | ![]() | 33 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pr6C ![]() 7pr7C ![]() 7pr8C ![]() 7pr9C ![]() 7prbC ![]() 7prtC ![]() 7psiC ![]() 7psjC ![]() 7pskC ![]() 5g0mS S: Starting model for refinement 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 50814.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 51196 / DSM 11244 / JCM 7670 / NBRC 15755 / NCIMB 13165 / 161 Gene: ACP_2665 / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.5 M AmSO4 1 M LiSO4 0.1 M Trisodium Citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91188 Å / Relative weight: 1 |
Reflection | Resolution: 1.24→74.69 Å / Num. obs: 134306 / % possible obs: 97.2 % / Redundancy: 6.1 % / CC1/2: 0.998 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.26→1.26 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6247 / CC1/2: 0.794 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5g0m Resolution: 1.24→74.69 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / Cross valid method: FREE R-VALUE / ESU R: 0.04 / ESU R Free: 0.042 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: 16.347 Å2
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Refinement step | Cycle: LAST / Resolution: 1.24→74.69 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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