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- PDB-7psk: Crystal structure of beta-glucuronidase from Acidobacterium capsu... -

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Basic information

Entry
Database: PDB / ID: 7psk
TitleCrystal structure of beta-glucuronidase from Acidobacterium capsulatum in complex with covalent inhibitor GR109
ComponentsBeta-glucuronidase
KeywordsCARBOHYDRATE / glycoside hydrolase / glucuronidase / GH79 / heparan sulfate
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / membrane
Similarity search - Function
Beta-glucuronidase, C-terminal / Glycosyl hydrolase family 79 C-terminal beta domain / : / Glycoside hydrolase, family 79 / Glycosyl hydrolase family 79, N-terminal domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Beta-glucuronidase C-terminal domain-containing protein
Similarity search - Component
Biological speciesAcidobacterium capsulatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsArmstrong, Z. / Wu, L. / Davies, G.J.
Funding support United Kingdom, 7items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2011-AdG-290836 United Kingdom
European Research Council (ERC)ERC-2012-AdG-322942 United Kingdom
Netherlands Organisation for Scientific Research (NWO) United Kingdom
Israel Science Foundation1021/19 United Kingdom
European Molecular Biology Organization (EMBO)STF8184 United Kingdom
Royal Society United Kingdom
Wellcome Trust218579/Z/19/Z United Kingdom
CitationJournal: 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
DepositionSep 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3062
Polymers50,8151
Non-polymers4911
Water10,196566
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.889, 44.573, 136.897
Angle α, β, γ (deg.)90.000, 97.599, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-920-

HOH

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Components

#1: Protein Beta-glucuronidase


Mass: 50814.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidobacterium capsulatum (strain ATCC 51196 / DSM 11244 / JCM 7670 / NBRC 15755 / NCIMB 13165 / 161) (bacteria)
Strain: ATCC 51196 / DSM 11244 / JCM 7670 / NBRC 15755 / NCIMB 13165 / 161
Gene: ACP_2665 / Production host: Escherichia coli (E. coli) / References: UniProt: C1F2K5
#2: Polysaccharide 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-(2R,3S,5R,6R)-2,3,4,5,6-pentakis(oxidanyl) ...2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-(2R,3S,5R,6R)-2,3,4,5,6-pentakis(oxidanyl)cyclohexane-1-carboxylic acid


Type: oligosaccharide / Mass: 491.422 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/1,1,0/[a2122h-1a_1-5_1*OC^RC^SC^RC^SC^SC^R$3/8O/7O/6O/5O/4CO/13=O_2*NCC/3=O_6*OSO/3=O/3=O]/1/WURCSPDB2Glycan 1.1.0
[][<C7O5>]{[(1+1)][a-D-GlcpNAc6SO3]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 566 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.5 M AmSO4 1 M LiSO4 0.1 M Trisodium Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91188 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91188 Å / Relative weight: 1
ReflectionResolution: 1.09→67.85 Å / Num. obs: 201068 / % possible obs: 97.6 % / Redundancy: 3.8 % / CC1/2: 0.994 / Net I/σ(I): 7.9
Reflection shellResolution: 1.09→1.11 Å / Num. unique obs: 9095 / CC1/2: 0.803

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5g0m

5g0m


Resolution: 1.09→42.383 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.193 / WRfactor Rwork: 0.178 / SU B: 0.42 / SU ML: 0.021 / Average fsc free: 0.9383 / Average fsc work: 0.9435 / Cross valid method: FREE R-VALUE / ESU R: 0.029 / ESU R Free: 0.03
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1849 9956 4.953 %
Rwork0.1719 191040 -
all0.173 --
obs-200996 97.342 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 11.154 Å2
Baniso -1Baniso -2Baniso -3
1--0.334 Å20 Å20.162 Å2
2--0.366 Å2-0 Å2
3----0.073 Å2
Refinement stepCycle: LAST / Resolution: 1.09→42.383 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3323 0 36 566 3925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0133547
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173161
X-RAY DIFFRACTIONr_angle_refined_deg1.9911.6644849
X-RAY DIFFRACTIONr_angle_other_deg1.6921.5827329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg18.6575.452476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.82722.093172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.52515495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3221520
X-RAY DIFFRACTIONr_chiral_restr0.1150.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024560
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02788
X-RAY DIFFRACTIONr_nbd_refined0.2650.2812
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.23239
X-RAY DIFFRACTIONr_nbtor_refined0.1930.21818
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0960.21788
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2421
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0330.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1380.211
X-RAY DIFFRACTIONr_nbd_other0.1810.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2810.230
X-RAY DIFFRACTIONr_mcbond_it1.0920.9871804
X-RAY DIFFRACTIONr_mcbond_other1.0890.9871803
X-RAY DIFFRACTIONr_mcangle_it1.5731.4852266
X-RAY DIFFRACTIONr_mcangle_other1.5731.4852267
X-RAY DIFFRACTIONr_scbond_it1.9481.1691743
X-RAY DIFFRACTIONr_scbond_other1.9481.1681744
X-RAY DIFFRACTIONr_scangle_it2.861.6882582
X-RAY DIFFRACTIONr_scangle_other2.8591.6882583
X-RAY DIFFRACTIONr_lrange_it4.09913.6754398
X-RAY DIFFRACTIONr_lrange_other3.81912.7934214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.09-1.1180.2657450.24213147X-RAY DIFFRACTION91.473
1.118-1.1490.2386870.22413495X-RAY DIFFRACTION95.8243
1.149-1.1820.237110.20813141X-RAY DIFFRACTION96.2078
1.182-1.2190.2076230.19312864X-RAY DIFFRACTION96.5564
1.219-1.2590.1886540.17912496X-RAY DIFFRACTION96.8907
1.259-1.3030.1886200.1712169X-RAY DIFFRACTION97.2326
1.303-1.3520.1936250.16611710X-RAY DIFFRACTION97.3099
1.352-1.4070.1735240.16211352X-RAY DIFFRACTION97.4561
1.407-1.470.1865740.15910842X-RAY DIFFRACTION97.531
1.47-1.5410.1625560.14910438X-RAY DIFFRACTION97.6724
1.541-1.6250.1584880.1539980X-RAY DIFFRACTION98.578
1.625-1.7230.1765410.1529430X-RAY DIFFRACTION98.8892
1.723-1.8420.1844550.1538987X-RAY DIFFRACTION99.2328
1.842-1.990.1694170.1568353X-RAY DIFFRACTION99.3655
1.99-2.1790.1664240.1597722X-RAY DIFFRACTION99.5357
2.179-2.4360.1663740.166997X-RAY DIFFRACTION99.7024
2.436-2.8130.1833410.1686204X-RAY DIFFRACTION99.9237
2.813-3.4440.1872520.1825285X-RAY DIFFRACTION99.8557
3.444-4.8650.1872170.1734108X-RAY DIFFRACTION99.7233
4.865-42.30.2141280.2292320X-RAY DIFFRACTION99.3506

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