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- PDB-8b0e: Crystal structure of beta-glucuronidase from Acidobacterium capsu... -

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Basic information

Entry
Database: PDB / ID: 8b0e
TitleCrystal structure of beta-glucuronidase from Acidobacterium capsulatum in complex with covalent inhibitor VB158
Componentsbeta-glucuronidase from Acidobacterium capsulatum
KeywordsHYDROLASE / b-glucuronidase
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-OV3 / Beta-glucuronidase C-terminal domain-containing protein
Similarity search - Component
Biological speciesAcidobacterium capsulatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsArmstrong, Z. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Chemmedchem / Year: 2023
Title: 4-O-Substituted Glucuronic Cyclophellitols are Selective Mechanism-Based Heparanase Inhibitors.
Authors: Borlandelli, V. / Armstrong, Z. / Nin-Hill, A. / Codee, J.D.C. / Raich, L. / Artola, M. / Rovira, C. / Davies, G.J. / Overkleeft, H.S.
History
DepositionSep 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 1, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 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
AAA: beta-glucuronidase from Acidobacterium capsulatum
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1462
Polymers50,8151
Non-polymers3311
Water5,981332
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.829, 44.476, 137.577
Angle α, β, γ (deg.)90.000, 97.629, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11AAA-652-

HOH

21AAA-827-

HOH

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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)
Strain: ATCC 51196 / DSM 11244 / BCRC 80197 / JCM 7670 / NBRC 15755 / NCIMB 13165 / 161
Gene: ACP_2665 / Production host: Escherichia coli (E. coli) / References: UniProt: C1F2K5
#2: Chemical ChemComp-OV3 / (1~{S},2~{R},3~{R},4~{S},6~{S})-3,4,6-tris(oxidanyl)-2-[2-[2,2,2-tris(fluoranyl)ethanoylamino]ethoxy]cyclohexane-1-carboxylic acid


Mass: 331.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16F3NO7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.5 Å3/Da / Density % sol: 50.82 %
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: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.55→39.21 Å / Num. obs: 70791 / % possible obs: 96.8 % / Redundancy: 5.8 % / CC1/2: 0.966 / Net I/σ(I): 2.9
Reflection shellResolution: 1.55→1.58 Å / Num. unique obs: 3423 / CC1/2: 0.616

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Processing

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

5g0m


Resolution: 1.55→39.21 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.836 / SU ML: 0.096 / Cross valid method: FREE R-VALUE / ESU R: 0.094 / ESU R Free: 0.095
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2519 3509 4.963 %
Rwork0.2198 67196 -
all0.221 --
obs-70705 96.362 %
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: 19.243 Å2
Baniso -1Baniso -2Baniso -3
1--1.158 Å2-0 Å20.444 Å2
2--1.952 Å2-0 Å2
3----0.881 Å2
Refinement stepCycle: LAST / Resolution: 1.55→39.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3341 0 22 332 3695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133491
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173116
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.6494761
X-RAY DIFFRACTIONr_angle_other_deg1.3991.5717219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5945445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.26821.844179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18215505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0631522
X-RAY DIFFRACTIONr_chiral_restr0.0750.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024025
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02778
X-RAY DIFFRACTIONr_nbd_refined0.2020.2605
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.22765
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21670
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21482
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2242
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1530.211
X-RAY DIFFRACTIONr_nbd_other0.1650.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1640.220
X-RAY DIFFRACTIONr_mcbond_it1.4911.9241777
X-RAY DIFFRACTIONr_mcbond_other1.4911.9231776
X-RAY DIFFRACTIONr_mcangle_it2.3312.8792223
X-RAY DIFFRACTIONr_mcangle_other2.332.8792224
X-RAY DIFFRACTIONr_scbond_it1.9832.1281714
X-RAY DIFFRACTIONr_scbond_other1.9792.1251710
X-RAY DIFFRACTIONr_scangle_it3.0353.1242538
X-RAY DIFFRACTIONr_scangle_other3.0363.1212536
X-RAY DIFFRACTIONr_lrange_it4.75923.0273865
X-RAY DIFFRACTIONr_lrange_other4.66922.6583793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.3132560.3164850X-RAY DIFFRACTION94.731
1.59-1.6340.3152620.2994688X-RAY DIFFRACTION94.8094
1.634-1.6810.3342230.2894666X-RAY DIFFRACTION95.5629
1.681-1.7330.3282200.2844486X-RAY DIFFRACTION95.2246
1.733-1.790.3132240.2744406X-RAY DIFFRACTION95.6216
1.79-1.8520.312440.264211X-RAY DIFFRACTION95.8271
1.852-1.9220.2721850.2424134X-RAY DIFFRACTION96.0205
1.922-2.0010.2772180.2283929X-RAY DIFFRACTION95.9732
2.001-2.090.2592190.2313793X-RAY DIFFRACTION96.4887
2.09-2.1920.271980.2173668X-RAY DIFFRACTION96.6742
2.192-2.310.2921610.2143508X-RAY DIFFRACTION97.0635
2.31-2.450.2551920.2093278X-RAY DIFFRACTION96.6843
2.45-2.6190.2281670.2013116X-RAY DIFFRACTION97.5342
2.619-2.8280.2241530.1942921X-RAY DIFFRACTION97.7114
2.828-3.0980.2651280.2152721X-RAY DIFFRACTION98.2753
3.098-3.4630.21200.1992473X-RAY DIFFRACTION98.4434
3.463-3.9970.1891030.1752214X-RAY DIFFRACTION98.6377
3.997-4.8920.2121090.191834X-RAY DIFFRACTION97.7364
4.892-6.9040.24770.2061460X-RAY DIFFRACTION99.0335
6.904-39.210.243500.232840X-RAY DIFFRACTION98.1257

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