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- PDB-8pej: CjGH35 with a Galactosidase Activity-Based Probe -

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Basic information

Entry
Database: PDB / ID: 8pej
TitleCjGH35 with a Galactosidase Activity-Based Probe
ComponentsBeta-galactosidase, putative, bgl35A
KeywordsHYDROLASE / Beta-galactosidase / Complex / Activity-based Probe
Function / homology
Function and homology information


beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
Domain of unknown function DUF5597 / Domain of unknown function (DUF5597) / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ACETATE ION / Chem-YGX / Beta-galactosidase, putative, bgl35A
Similarity search - Component
Biological speciesCellvibrio japonicus Ueda107 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsOffen, W.A. / Davies, G.J.
Funding support United Kingdom, European Union, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R001162/1 United Kingdom
European Research Council (ERC)951231European Union
CitationJournal: Org.Biomol.Chem. / Year: 2023
Title: The development of a broad-spectrum retaining beta-exo-galactosidase activity-based probe.
Authors: Kuo, C.L. / Su, Q. / van den Nieuwendijk, A.M.C.H. / Beenakker, T.J.M. / Offen, W.A. / Willems, L.I. / Boot, R.G. / Sarris, A.J. / Marques, A.R.A. / Codee, J.D.C. / van der Marel, G.A. / ...Authors: Kuo, C.L. / Su, Q. / van den Nieuwendijk, A.M.C.H. / Beenakker, T.J.M. / Offen, W.A. / Willems, L.I. / Boot, R.G. / Sarris, A.J. / Marques, A.R.A. / Codee, J.D.C. / van der Marel, G.A. / Florea, B.I. / Davies, G.J. / Overkleeft, H.S. / Aerts, J.M.F.G.
History
DepositionJun 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 2.0Jul 1, 2026Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_validate_rmsd_bond / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_modification_feature.modified_residue_id_linking_atom / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_validate_rmsd_bond.auth_atom_id_2 / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _struct_conn.ptnr1_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-galactosidase, putative, bgl35A
B: Beta-galactosidase, putative, bgl35A
C: Beta-galactosidase, putative, bgl35A
D: Beta-galactosidase, putative, bgl35A
E: Beta-galactosidase, putative, bgl35A
F: Beta-galactosidase, putative, bgl35A
G: Beta-galactosidase, putative, bgl35A
H: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)500,20165
Polymers497,0168
Non-polymers3,18557
Water79,5004413
1
A: Beta-galactosidase, putative, bgl35A
B: Beta-galactosidase, putative, bgl35A
C: Beta-galactosidase, putative, bgl35A
H: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,80726
Polymers248,5084
Non-polymers1,29922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13110 Å2
ΔGint-183 kcal/mol
Surface area78390 Å2
MethodPISA
2
D: Beta-galactosidase, putative, bgl35A
E: Beta-galactosidase, putative, bgl35A
F: Beta-galactosidase, putative, bgl35A
G: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,39439
Polymers248,5084
Non-polymers1,88635
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14130 Å2
ΔGint-219 kcal/mol
Surface area78630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.316, 116.212, 116.396
Angle α, β, γ (deg.)90.236, 89.889, 90.094
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Beta-galactosidase, putative, bgl35A


Mass: 62127.023 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: beta-galactosidase without signal peptide and with N-terminal hexahistidine tag
Source: (gene. exp.) Cellvibrio japonicus Ueda107 (bacteria)
Gene: bgl35A, CJA_2707 / Production host: Escherichia coli (E. coli) / References: UniProt: B3PBE0, beta-galactosidase
#2: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-YGX / (1S,2S,4S,5R)-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol / Beta-galactose-configured cyclophellitol (post-reaction)


Mass: 194.182 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H14O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4413 / 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: 2.71 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: Sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.5→99.32 Å / Num. obs: 802827 / % possible obs: 96.3 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.043 / Rrim(I) all: 0.061 / Net I/σ(I): 10.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.0467 / Mean I/σ(I) obs: 2 / Num. unique obs: 37248 / CC1/2: 0.719 / Rpim(I) all: 0.0467 / Rrim(I) all: 0.66 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
REFMAC5.8.0411refinement
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→82.544 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.198 / SU ML: 0.044 / Cross valid method: FREE R-VALUE / ESU R: 0.061 / ESU R Free: 0.063
Details: Hydrogens have been added in their riding positions There was incomplete electron density for loop 434 - 445, which has been modelled at partial occupancy or left partially unmodelled for each chain.
RfactorNum. reflection% reflection
Rfree0.181 40267 5.016 %
Rwork0.1566 762488 -
all0.158 --
obs-762488 96.256 %
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: 21.647 Å2
Baniso -1Baniso -2Baniso -3
1-1.202 Å2-0.143 Å20.182 Å2
2---0.43 Å20.126 Å2
3----0.771 Å2
Refinement stepCycle: LAST / Resolution: 1.5→82.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33749 0 187 4413 38349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01235542
X-RAY DIFFRACTIONr_bond_other_d0.0010.01632682
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.64948565
X-RAY DIFFRACTIONr_angle_other_deg0.5681.56775109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.09454457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.9865206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.821105427
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.172101661
X-RAY DIFFRACTIONr_chiral_restr0.0890.25223
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0242424
X-RAY DIFFRACTIONr_gen_planes_other0.0010.028457
X-RAY DIFFRACTIONr_nbd_refined0.2280.26755
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.228690
X-RAY DIFFRACTIONr_nbtor_refined0.1850.217141
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.218084
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.23402
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0290.25
X-RAY DIFFRACTIONr_metal_ion_refined0.1150.248
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1890.243
X-RAY DIFFRACTIONr_nbd_other0.3060.2114
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.210.236
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1010.27
X-RAY DIFFRACTIONr_mcbond_it1.9762.30517620
X-RAY DIFFRACTIONr_mcbond_other1.9742.30517607
X-RAY DIFFRACTIONr_mcangle_it2.6364.14122116
X-RAY DIFFRACTIONr_mcangle_other2.6364.14122117
X-RAY DIFFRACTIONr_scbond_it2.8612.47517922
X-RAY DIFFRACTIONr_scbond_other2.8612.47517923
X-RAY DIFFRACTIONr_scangle_it4.0934.44926442
X-RAY DIFFRACTIONr_scangle_other4.0934.44926443
X-RAY DIFFRACTIONr_lrange_it5.09524.71541430
X-RAY DIFFRACTIONr_lrange_other4.90323.78740048
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.5-1.5390.25328160.238528580.239616060.9530.95890.37110.239
1.539-1.5810.23428470.216537600.217602490.9620.96793.95510.215
1.581-1.6270.22328110.196529120.197584510.9660.97395.33280.192
1.627-1.6770.21527050.186515390.188567390.970.97895.60270.181
1.677-1.7320.225970.175502000.177550660.9750.98195.87950.169
1.732-1.7930.20625200.169486270.171532060.9730.98296.13010.163
1.793-1.860.20225480.163468920.165513670.9740.98396.24860.158
1.86-1.9360.19123800.161454280.163495390.9760.98396.50580.158
1.936-2.0220.19323860.159432940.161472470.9770.98496.68340.158
2.022-2.1210.18522350.155418210.157453360.9790.98597.17660.157
2.121-2.2360.17120420.148398740.149430870.9820.98797.28220.152
2.236-2.3710.17819080.146376690.148407750.980.98797.06190.153
2.371-2.5350.17318990.143355690.145382780.9810.98797.88390.154
2.535-2.7370.18517650.152332430.154356190.9790.98698.28460.167
2.737-2.9980.18516330.161307370.162328510.9790.98498.53580.18
2.998-3.3520.1814170.16276320.161295390.9820.98698.34120.18
3.352-3.8690.1613110.141246030.142261730.9850.98999.01040.166
3.869-4.7360.13710820.118207960.119220610.990.99299.17050.146
4.736-6.6870.1698970.156161330.156171190.9870.9999.48010.19
6.687-82.5440.2254690.21989010.21994060.9740.97599.61730.309

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