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- PDB-5g0q: beta-glucuronidase with an activity-based probe (N-alkyl cyclophe... -

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Basic information

Entry
Database: PDB / ID: 5g0q
Titlebeta-glucuronidase with an activity-based probe (N-alkyl cyclophellitol aziridine) bound
ComponentsBETA-GLUCURONIDASE
KeywordsHYDROLASE / GH79 / BETA-GLUCURONIDASE / ACTIVITY-BASED PROBE / RETAINING ENZYME
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 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Beta-glucuronidase, C-terminal / Glycosyl hydrolase family 79 C-terminal beta domain / : / Glycoside hydrolase, family 79 / Glycosyl hydrolase family 79, N-terminal domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-IF6 / Beta-glucuronidase C-terminal domain-containing protein
Similarity search - Component
Biological speciesACIDOBACTERIUM CAPSULATUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsJin, Y. / Wu, L. / Jiang, J.B. / Overkleeft, H.S. / Davies, G.J.
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Activity-based probes for functional interrogation of retaining beta-glucuronidases.
Authors: Wu, L. / Jiang, J. / Jin, Y. / Kallemeijn, W.W. / Kuo, C.L. / Artola, M. / Dai, W. / van Elk, C. / van Eijk, M. / van der Marel, G.A. / Codee, J.D.C. / Florea, B.I. / Aerts, J.M.F.G. / ...Authors: Wu, L. / Jiang, J. / Jin, Y. / Kallemeijn, W.W. / Kuo, C.L. / Artola, M. / Dai, W. / van Elk, C. / van Eijk, M. / van der Marel, G.A. / Codee, J.D.C. / Florea, B.I. / Aerts, J.M.F.G. / Overkleeft, H.S. / Davies, G.J.
History
DepositionMar 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-GLUCURONIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3604
Polymers50,8151
Non-polymers5463
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)148.512, 44.896, 82.216
Angle α, β, γ (deg.)90.00, 114.78, 90.00
Int Tables number5
Space group name H-MC121

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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 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: C1F2K5, beta-glucuronidase
#2: Chemical ChemComp-IF6 / (1R,2S,3R,4S,5S,6R)-7-(8-AZIDOOCTYL)-3,4,5-TRIHYDROXY-


Mass: 361.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H29N4O6
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
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: 2.45 Å3/Da / Density % sol: 49.77 % / Description: NONE
Crystal growpH: 8.6 / Details: 8.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97949
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Oct 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.65→42.6 Å / Num. obs: 59263 / % possible obs: 99.5 % / Observed criterion σ(I): 2.2 / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.1
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 4 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VO0

3vo0


Resolution: 1.65→74.64 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.967 / SU B: 3.765 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16922 2907 4.9 %RANDOM
Rwork0.12046 ---
obs0.12289 56355 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 1.65→74.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3428 0 36 294 3758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193562
X-RAY DIFFRACTIONr_bond_other_d0.0030.023265
X-RAY DIFFRACTIONr_angle_refined_deg1.8591.964852
X-RAY DIFFRACTIONr_angle_other_deg1.30837509
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1915455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55824.013157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67615502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.951518
X-RAY DIFFRACTIONr_chiral_restr0.1220.2523
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214137
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02835
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8231.7211820
X-RAY DIFFRACTIONr_mcbond_other2.8231.721821
X-RAY DIFFRACTIONr_mcangle_it3.4212.5912272
X-RAY DIFFRACTIONr_mcangle_other3.4222.5922273
X-RAY DIFFRACTIONr_scbond_it4.0612.1141742
X-RAY DIFFRACTIONr_scbond_other4.0592.1131742
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4783.0132580
X-RAY DIFFRACTIONr_long_range_B_refined4.94615.434208
X-RAY DIFFRACTIONr_long_range_B_other4.94415.434208
X-RAY DIFFRACTIONr_rigid_bond_restr3.23136827
X-RAY DIFFRACTIONr_sphericity_free30.578586
X-RAY DIFFRACTIONr_sphericity_bonded13.3656943
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 237 -
Rwork0.259 4072 -
obs--99.33 %

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