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

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Basic information

Entry
Database: PDB / ID: 7psh
TitleCrystal structure of beta-glucuronidase from Acidobacterium capsulatum at 1.24 Angstrom resolution
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: 1.24 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-glucuronidase


Theoretical massNumber of molelcules
Total (without water)50,8151
Polymers50,8151
Non-polymers00
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.865, 44.149, 136.277
Angle α, β, γ (deg.)90.000, 97.577, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-631-

HOH

21A-869-

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.43 Å3/Da / Density % sol: 49.41 %
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: 1.24→74.69 Å / Num. obs: 134306 / % possible obs: 97.2 % / Redundancy: 6.1 % / CC1/2: 0.998 / Net I/σ(I): 11.6
Reflection shellResolution: 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

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

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
RfactorNum. reflection% reflection
Rfree0.1878 6827 5.085 %
Rwork0.1686 127431 -
all0.17 --
obs-134258 96.845 %
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: 16.347 Å2
Baniso -1Baniso -2Baniso -3
1--0.922 Å2-0 Å20.17 Å2
2--0.688 Å2-0 Å2
3---0.183 Å2
Refinement stepCycle: LAST / Resolution: 1.24→74.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 5 411 3788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0133524
X-RAY DIFFRACTIONr_bond_other_d0.0360.0173154
X-RAY DIFFRACTIONr_angle_refined_deg1.9591.6484805
X-RAY DIFFRACTIONr_angle_other_deg2.4051.5727300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3155456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.54721.854178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17415509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4241522
X-RAY DIFFRACTIONr_chiral_restr0.1030.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024089
X-RAY DIFFRACTIONr_gen_planes_other0.020.02789
X-RAY DIFFRACTIONr_nbd_refined0.2320.2731
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2210.23061
X-RAY DIFFRACTIONr_nbtor_refined0.1910.21787
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21703
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2294
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1210.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1630.218
X-RAY DIFFRACTIONr_nbd_other0.2170.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2120.217
X-RAY DIFFRACTIONr_mcbond_it1.61.5731816
X-RAY DIFFRACTIONr_mcbond_other1.61.5731815
X-RAY DIFFRACTIONr_mcangle_it2.2892.3612273
X-RAY DIFFRACTIONr_mcangle_other2.2892.3622274
X-RAY DIFFRACTIONr_scbond_it2.5631.7951708
X-RAY DIFFRACTIONr_scbond_other2.5621.7951709
X-RAY DIFFRACTIONr_scangle_it3.7632.6042531
X-RAY DIFFRACTIONr_scangle_other3.7622.6052532
X-RAY DIFFRACTIONr_lrange_it4.92319.584146
X-RAY DIFFRACTIONr_lrange_other4.8519.0974049
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.24-1.2720.2844360.24485860.246101680.8330.84288.72930.228
1.272-1.3070.2274880.22389180.22399380.90.89794.64680.207
1.307-1.3450.2414590.21288310.21396680.9030.9196.09020.197
1.345-1.3860.2164710.20485970.20594140.9180.92296.32460.189
1.386-1.4320.2174650.19183230.19290980.9260.93396.59270.175
1.432-1.4820.1964590.17780600.17887920.9430.94796.89490.163
1.482-1.5380.1794510.16178300.16285160.9550.95697.24050.15
1.538-1.6010.1934050.16675340.16881510.9480.95597.39910.157
1.601-1.6720.1874100.16173080.16279020.9530.95997.67150.155
1.672-1.7530.1893710.1669800.16175100.9530.95897.88280.156
1.753-1.8480.183560.15866590.15971810.9570.96297.68830.159
1.848-1.960.1643350.15663060.15767520.9650.96698.3560.162
1.96-2.0950.1842930.1659950.16163700.9560.96398.71270.172
2.095-2.2630.1832940.15255800.15359380.960.96698.92220.167
2.263-2.4790.1672720.15251680.15254880.9670.96999.12540.173
2.479-2.7710.1712420.16147170.16249930.9630.96699.3190.188
2.771-3.1990.1812190.17541360.17643770.960.95999.49740.21
3.199-3.9160.1821890.15935440.1637480.9640.96799.59980.196
3.916-5.5310.171250.15727980.15729310.9680.96999.72710.2
5.531-74.6930.252870.22415630.22516620.9350.94299.2780.296

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