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- PDB-8ohx: Crystal structure of Beta-glucuronidase from Escherichia coli in ... -

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Basic information

Entry
Database: PDB / ID: 8ohx
TitleCrystal structure of Beta-glucuronidase from Escherichia coli in complex with siastatin B derived inhibitor
ComponentsBeta-D-glucuronidase
KeywordsHYDROLASE / Inhibitor / Complex
Function / homology
Function and homology information


beta-glucuronidase / beta-glucuronidase activity / carbohydrate metabolic process
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 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 ...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 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-VON / Beta-D-glucuronidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsArmstrong, Z. / Yurong, C. / Wu, L. / Overkleeft, H.S. / Davies, G.J.
Funding support Netherlands, European Union, United Kingdom, 6items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)VI.Veni.212.173 Netherlands
European Research Council (ERC)ERC-2011-AdG-290836European Union
European Research Council (ERC)ERC-2012-AdG-32294European Union
European Research Council (ERC)ERC-2020-SyG-951231European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R001162/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011151/1 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Molecular Basis for Inhibition of Heparanases and beta-Glucuronidases by Siastatin B.
Authors: Chen, Y. / van den Nieuwendijk, A.M.C.H. / Wu, L. / Moran, E. / Skoulikopoulou, F. / van Riet, V. / Overkleeft, H.S. / Davies, G.J. / Armstrong, Z.
History
DepositionMar 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)137,1054
Polymers136,7512
Non-polymers3542
Water5,621312
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-15 kcal/mol
Surface area43890 Å2
Unit cell
Length a, b, c (Å)126.281, 76.711, 141.018
Angle α, β, γ (deg.)90.000, 102.010, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Beta-D-glucuronidase


Mass: 68375.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: uidA, BN877_II1269 / Production host: Escherichia coli (E. coli) / References: UniProt: U4Q148, beta-glucuronidase
#2: Chemical ChemComp-VON / (3~{S},4~{S},5~{S},6~{R})-4,5,6-tris(oxidanyl)piperidine-3-carboxylic acid


Mass: 177.155 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 49.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
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: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→67.04 Å / Num. obs: 94487 / % possible obs: 98.4 % / Redundancy: 4.1 % / CC1/2: 0.997 / Net I/σ(I): 8.1
Reflection shellResolution: 1.95→1.98 Å / Num. unique obs: 4628 / CC1/2: 0.717

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→61.835 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.343 / WRfactor Rwork: 0.245 / SU B: 7.175 / SU ML: 0.192 / Average fsc free: 0.7935 / Average fsc work: 0.817 / Cross valid method: FREE R-VALUE / ESU R: 0.195 / ESU R Free: 0.188
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2847 4644 4.916 %
Rwork0.2206 89827 -
all0.224 --
obs-94471 98.229 %
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: 49.837 Å2
Baniso -1Baniso -2Baniso -3
1--1.065 Å2-0 Å2-0.735 Å2
2--4.979 Å20 Å2
3----3.302 Å2
Refinement stepCycle: LAST / Resolution: 1.95→61.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9538 0 24 312 9874
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0139837
X-RAY DIFFRACTIONr_bond_other_d0.0020.0178685
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.64113389
X-RAY DIFFRACTIONr_angle_other_deg1.3321.57720135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.99551187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38622.827566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.886151564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8771558
X-RAY DIFFRACTIONr_chiral_restr0.0690.21240
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211157
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022169
X-RAY DIFFRACTIONr_nbd_refined0.2080.22002
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.28544
X-RAY DIFFRACTIONr_nbtor_refined0.1710.24566
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.24217
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2424
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1250.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1960.222
X-RAY DIFFRACTIONr_nbd_other0.2410.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1280.212
X-RAY DIFFRACTIONr_mcbond_it3.8265.2894757
X-RAY DIFFRACTIONr_mcbond_other3.8265.2884756
X-RAY DIFFRACTIONr_mcangle_it5.3377.9135941
X-RAY DIFFRACTIONr_mcangle_other5.3377.9155942
X-RAY DIFFRACTIONr_scbond_it3.6665.5015080
X-RAY DIFFRACTIONr_scbond_other3.6665.5015081
X-RAY DIFFRACTIONr_scangle_it5.4048.1587448
X-RAY DIFFRACTIONr_scangle_other5.4048.1577449
X-RAY DIFFRACTIONr_lrange_it7.33159.63511027
X-RAY DIFFRACTIONr_lrange_other7.32559.62510969
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.0010.3733400.3536549X-RAY DIFFRACTION97.2748
2.001-2.0550.3783230.3356402X-RAY DIFFRACTION97.2805
2.055-2.1150.3883290.3426189X-RAY DIFFRACTION97.4727
2.115-2.180.3513390.3156031X-RAY DIFFRACTION97.7444
2.18-2.2520.3812870.2915890X-RAY DIFFRACTION97.7064
2.252-2.3310.3532900.2755677X-RAY DIFFRACTION97.9964
2.331-2.4180.3212850.2525547X-RAY DIFFRACTION98.0827
2.418-2.5170.3042930.2555265X-RAY DIFFRACTION98.3021
2.517-2.6290.3162800.2575119X-RAY DIFFRACTION98.3604
2.629-2.7570.3142670.2534852X-RAY DIFFRACTION98.5371
2.757-2.9060.3212610.2554638X-RAY DIFFRACTION98.334
2.906-3.0820.3142260.254425X-RAY DIFFRACTION98.6426
3.082-3.2950.3061810.2354159X-RAY DIFFRACTION98.9061
3.295-3.5590.2852060.2413889X-RAY DIFFRACTION99.0326
3.559-3.8980.251660.2033585X-RAY DIFFRACTION99.1017
3.898-4.3570.2531570.1643270X-RAY DIFFRACTION99.2183
4.357-5.030.2151510.1532872X-RAY DIFFRACTION99.3428
5.03-6.1570.2041260.1672471X-RAY DIFFRACTION99.5401
6.157-8.6910.222840.151913X-RAY DIFFRACTION99.1559
8.691-61.8350.294530.1871084X-RAY DIFFRACTION98.4416

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