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- PDB-7pr6: Crystal structure of E. coli beta-glucuronidase in complex with c... -

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Basic information

Entry
Database: PDB / ID: 7pr6
TitleCrystal structure of E. coli beta-glucuronidase in complex with covalent inhibitor ME727
ComponentsBeta-glucuronidase
KeywordsCARBOHYDRATE / glycoside hydrolase / glucuronidase / GH2
Function / homology
Function and homology information


glucuronoside catabolic process / beta-glucuronidase / beta-glucuronidase activity / carbohydrate binding / carbohydrate metabolic process / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich ...Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-8I4 / Beta-glucuronidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsWu, L. / Armstrong, Z. / 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 20, 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

Downloads & links

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Assembly

Deposited unit
AAA: Beta-glucuronidase
BBB: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,1674
Polymers136,7512
Non-polymers4162
Water8,449469
1
AAA: Beta-glucuronidase
BBB: Beta-glucuronidase
hetero molecules

AAA: Beta-glucuronidase
BBB: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,3358
Polymers273,5024
Non-polymers8334
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area13120 Å2
ΔGint-88 kcal/mol
Surface area80570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.800, 76.580, 125.740
Angle α, β, γ (deg.)90.000, 125.010, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-glucuronidase / GUS / Beta-D-glucuronoside glucuronosohydrolase


Mass: 68375.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: uidA, gurA, gusA, b1617, JW1609 / Production host: Escherichia coli (E. coli) / References: UniProt: P05804, beta-glucuronidase
#2: Sugar ChemComp-8I4 / (2R,3S,5R,6R)-2,3,4,5,6-pentakis(oxidanyl)cyclohexane-1-carboxylic acid / (2R)-5-[(E)-2-(2,4-dinitrophenyl)ethenyl]-2-[(1R)-2-oxidanyl-2-oxidanylidene-1-(2-thiophen-2-ylethanoylamino)ethyl]-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid


Type: saccharide / Mass: 208.166 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H12O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Bis-Tris propane pH 7.5, 20% (w/v) PEG 3350, 0.2 M NaNO3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.99→47.76 Å / Num. obs: 86916 / % possible obs: 97.3 % / Redundancy: 3.9 % / CC1/2: 0.983 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.083 / Net I/σ(I): 6.5
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.695 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 6526 / CC1/2: 0.334 / Rpim(I) all: 0.983 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3k46

3k46


Resolution: 1.99→47.803 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.266 / WRfactor Rwork: 0.222 / Average fsc free: 0.8368 / Average fsc work: 0.8483 / Cross valid method: FREE R-VALUE / ESU R: 0.22 / ESU R Free: 0.188
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2631 4333 4.985 %
Rwork0.2209 82582 -
all0.223 --
obs-86915 96.893 %
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: 48.325 Å2
Baniso -1Baniso -2Baniso -3
1--1.766 Å2-0 Å2-0.283 Å2
2--1.572 Å2-0 Å2
3---0.298 Å2
Refinement stepCycle: LAST / Resolution: 1.99→47.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9566 0 26 469 10061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0139859
X-RAY DIFFRACTIONr_bond_other_d0.0350.0158948
X-RAY DIFFRACTIONr_angle_refined_deg1.7161.64213419
X-RAY DIFFRACTIONr_angle_other_deg2.3681.58220557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.09251188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67822.796565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33151571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5141558
X-RAY DIFFRACTIONr_chiral_restr0.0790.21246
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211337
X-RAY DIFFRACTIONr_gen_planes_other0.0160.022407
X-RAY DIFFRACTIONr_nbd_refined0.2020.21880
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2260.28629
X-RAY DIFFRACTIONr_nbtor_refined0.1710.24692
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.24465
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2469
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0640.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2810.218
X-RAY DIFFRACTIONr_nbd_other0.2730.292
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1840.219
X-RAY DIFFRACTIONr_mcbond_it2.0055.0694764
X-RAY DIFFRACTIONr_mcbond_other2.0055.0684763
X-RAY DIFFRACTIONr_mcangle_it3.067.5925948
X-RAY DIFFRACTIONr_mcangle_other3.067.5935949
X-RAY DIFFRACTIONr_scbond_it2.3215.2315095
X-RAY DIFFRACTIONr_scbond_other2.3215.2315096
X-RAY DIFFRACTIONr_scangle_it3.6377.7717471
X-RAY DIFFRACTIONr_scangle_other3.6367.7717472
X-RAY DIFFRACTIONr_lrange_it5.01256.27811029
X-RAY DIFFRACTIONr_lrange_other4.9856.24110958
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.0420.3633250.3516185X-RAY DIFFRACTION98.4276
2.042-2.0980.3732840.3336069X-RAY DIFFRACTION98.542
2.098-2.1580.3283210.315823X-RAY DIFFRACTION98.6038
2.158-2.2250.3353060.3025690X-RAY DIFFRACTION98.7809
2.225-2.2980.2912970.2865516X-RAY DIFFRACTION98.4753
2.298-2.3780.2942780.275344X-RAY DIFFRACTION98.6662
2.378-2.4680.2782700.2635182X-RAY DIFFRACTION98.8039
2.468-2.5690.272720.2474954X-RAY DIFFRACTION98.5294
2.569-2.6830.2892390.2484749X-RAY DIFFRACTION98.4603
2.683-2.8140.2722260.2394547X-RAY DIFFRACTION98.2301
2.814-2.9660.2862360.2354291X-RAY DIFFRACTION97.5016
2.966-3.1450.2932140.2494005X-RAY DIFFRACTION96.4122
3.145-3.3620.3052210.2443677X-RAY DIFFRACTION94.6116
3.362-3.6320.2752020.2243355X-RAY DIFFRACTION92.5098
3.632-3.9780.2261560.1933102X-RAY DIFFRACTION91.6198
3.978-4.4460.1951370.1572796X-RAY DIFFRACTION91.3707
4.446-5.1330.1961100.1482525X-RAY DIFFRACTION92.6186
5.133-6.2820.2071030.1732135X-RAY DIFFRACTION93.2889
6.282-8.8680.171780.1611686X-RAY DIFFRACTION93.284
8.868-47.8030.281580.165951X-RAY DIFFRACTION92.739

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