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- PDB-8ohv: Crystal structure of Beta-glucuronidase from Acidobacterium capsu... -

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Basic information

Entry
Database: PDB / ID: 8ohv
TitleCrystal structure of Beta-glucuronidase from Acidobacterium capsulatum in complex with glucuronic acid configured 3-geminal diol iminosugar inhibitor
Componentsbeta-glucuronidase from Acidobacterium capsulatum
KeywordsHYDROLASE / Inhibitor / Complex
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
Chem-VP5 / Beta-glucuronidase C-terminal domain-containing protein
Similarity search - Component
Biological speciesAcidobacterium capsulatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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-glucuronidase from Acidobacterium capsulatum
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0883
Polymers50,8151
Non-polymers2732
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-9 kcal/mol
Surface area17140 Å2
Unit cell
Length a, b, c (Å)82.037, 42.614, 140.141
Angle α, β, γ (deg.)90.000, 99.417, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein beta-glucuronidase from Acidobacterium capsulatum


Mass: 50814.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidobacterium capsulatum (bacteria) / Gene: ACP_2665 / Production host: Escherichia coli (E. coli) / References: UniProt: C1F2K5
#2: Chemical ChemComp-VP5 / (3~{S},4~{R})-4,5,5-tris(oxidanyl)piperidine-3-carboxylic acid


Mass: 177.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.38 Å3/Da / Density % sol: 48.27 %
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 / Wavelength: 0.979499 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979499 Å / Relative weight: 1
ReflectionResolution: 1.5→40.756 Å / Num. obs: 76979 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.999 / Net I/σ(I): 11
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 3804 / CC1/2: 0.545

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→40.756 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.194 / SU B: 1.674 / SU ML: 0.06 / Average fsc free: 0.8931 / Average fsc work: 0.9001 / Cross valid method: FREE R-VALUE / ESU R: 0.076 / ESU R Free: 0.076
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2231 3861 5.016 %
Rwork0.1989 73117 -
all0.2 --
obs-76978 99.949 %
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: 22.124 Å2
Baniso -1Baniso -2Baniso -3
1--0.264 Å2-0 Å20.532 Å2
2--0.871 Å20 Å2
3----0.743 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3417 0 17 182 3616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133543
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173162
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.6474829
X-RAY DIFFRACTIONr_angle_other_deg1.5241.5717315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8465454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.89921.878181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18715506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2621522
X-RAY DIFFRACTIONr_chiral_restr0.0860.2452
X-RAY DIFFRACTIONr_chiral_restr_other0.0080.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024096
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02790
X-RAY DIFFRACTIONr_nbd_refined0.2120.2686
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.22809
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21729
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21515
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.2137
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1090.210
X-RAY DIFFRACTIONr_nbd_other0.2220.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.140.27
X-RAY DIFFRACTIONr_mcbond_it2.0372.1651816
X-RAY DIFFRACTIONr_mcbond_other2.0322.1641814
X-RAY DIFFRACTIONr_mcangle_it2.8673.2412270
X-RAY DIFFRACTIONr_mcangle_other2.8673.2422271
X-RAY DIFFRACTIONr_scbond_it3.2692.5011727
X-RAY DIFFRACTIONr_scbond_other3.2692.4991724
X-RAY DIFFRACTIONr_scangle_it4.8813.6192559
X-RAY DIFFRACTIONr_scangle_other4.8813.6152554
X-RAY DIFFRACTIONr_lrange_it5.82425.4783894
X-RAY DIFFRACTIONr_lrange_other5.82525.3893873
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.3042830.2995384X-RAY DIFFRACTION99.8063
1.539-1.5810.2932830.2715227X-RAY DIFFRACTION100
1.581-1.6270.2772560.2555091X-RAY DIFFRACTION100
1.627-1.6770.2592710.2434940X-RAY DIFFRACTION99.9808
1.677-1.7320.2532490.2264770X-RAY DIFFRACTION99.9801
1.732-1.7930.2522530.2054657X-RAY DIFFRACTION100
1.793-1.860.2362300.1924525X-RAY DIFFRACTION100
1.86-1.9360.2012230.1774300X-RAY DIFFRACTION99.9779
1.936-2.0220.2092170.1834134X-RAY DIFFRACTION100
2.022-2.1210.2562050.1933965X-RAY DIFFRACTION100
2.121-2.2350.2271890.1883792X-RAY DIFFRACTION100
2.235-2.3710.2141960.1843583X-RAY DIFFRACTION100
2.371-2.5340.191760.1853347X-RAY DIFFRACTION100
2.534-2.7370.2391830.2013108X-RAY DIFFRACTION100
2.737-2.9980.2521560.2112899X-RAY DIFFRACTION100
2.998-3.3510.211330.2052620X-RAY DIFFRACTION100
3.351-3.8690.2131160.1812356X-RAY DIFFRACTION100
3.869-4.7350.1761000.1561995X-RAY DIFFRACTION100
4.735-6.6830.195970.2091523X-RAY DIFFRACTION100
6.683-40.7560.23450.217902X-RAY DIFFRACTION99.5794

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