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- PDB-5jaw: Structure of a beta galactosidase with inhibitor -

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Basic information

Entry
Database: PDB / ID: 5jaw
TitleStructure of a beta galactosidase with inhibitor
ComponentsBeta-galactosidase, putative, bgl35A
KeywordsHYDROLASE / beta galactosidase / inhibitor / aziridine
Function / homology
Function and homology information


beta-galactosidase complex / beta-galactosidase / vacuole / beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
putative beta-Galactosidase from caulobacter crescentus / Domain of unknown function DUF5597 / Domain of unknown function (DUF5597) / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Glycoside hydrolase, family 35 / Chondroitinase Ac; Chain A, domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...putative beta-Galactosidase from caulobacter crescentus / Domain of unknown function DUF5597 / Domain of unknown function (DUF5597) / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Glycoside hydrolase, family 35 / Chondroitinase Ac; Chain A, domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-UUU / Beta-galactosidase, putative, bgl35A
Similarity search - Component
Biological speciesCellvibrio japonicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsOffen, W. / Davies, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
CitationJournal: Chem. Commun. (Camb.) / Year: 2017
Title: Towards broad spectrum activity-based glycosidase probes: synthesis and evaluation of deoxygenated cyclophellitol aziridines.
Authors: Schroder, S.P. / van de Sande, J.W. / Kallemeijn, W.W. / Kuo, C.L. / Artola, M. / van Rooden, E.J. / Jiang, J. / Beenakker, T.J.M. / Florea, B.I. / Offen, W.A. / Davies, G.J. / Minnaard, A.J. ...Authors: Schroder, S.P. / van de Sande, J.W. / Kallemeijn, W.W. / Kuo, C.L. / Artola, M. / van Rooden, E.J. / Jiang, J. / Beenakker, T.J.M. / Florea, B.I. / Offen, W.A. / Davies, G.J. / Minnaard, A.J. / Aerts, J.M.F.G. / Codee, J.D.C. / van der Marel, G.A. / Overkleeft, H.S.
History
DepositionApr 12, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 11, 2020Group: Derived calculations / Refinement description
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist
Item: _refine_hist.d_res_high
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.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)499,19642
Polymers497,0168
Non-polymers2,17934
Water29,4731636
1
C: Beta-galactosidase, putative, bgl35A
E: Beta-galactosidase, putative, bgl35A
hetero molecules

A: Beta-galactosidase, putative, bgl35A
D: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,68524
Polymers248,5084
Non-polymers1,17720
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area12310 Å2
ΔGint-173 kcal/mol
Surface area76080 Å2
MethodPISA
2
B: Beta-galactosidase, putative, bgl35A
F: Beta-galactosidase, putative, bgl35A
hetero molecules

G: Beta-galactosidase, putative, bgl35A
H: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,51118
Polymers248,5084
Non-polymers1,00314
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area11380 Å2
ΔGint-121 kcal/mol
Surface area75290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.168, 115.660, 115.935
Angle α, β, γ (deg.)90.15, 90.11, 90.11
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: N-terminally his tagged construct without predicted native signal peptide
Source: (gene. exp.) Cellvibrio japonicus (strain Ueda107) (bacteria)
Strain: Ueda107 / Gene: bgl35A, CJA_2707 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B3PBE0, beta-galactosidase
#2: Chemical
ChemComp-UUU / (1S,2S,3S,4S,5R,6R)-5-amino-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol


Mass: 193.198 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H15NO5
#3: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1636 / Source method: isolated from a natural source / Formula: H2O

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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: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 2.7 M Na acetate pH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 21, 2016
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.649
11h,-k,-l20.052
11H, L, -K30.142
11H, -L, K40.158
ReflectionResolution: 1.6→81.99 Å / Num. obs: 650665 / % possible obs: 95.7 % / Redundancy: 1.8 % / CC1/2: 0.979 / Rmerge(I) obs: 0.08 / Net I/σ(I): 6
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 1.2 / % possible all: 94.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4d1i

4d1i


Resolution: 1.6→81.99 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.024 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.019 / ESU R Free: 0.018
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE IS INSUFFICIENT DENSITY TO ALLOW RELIABLE MODELLING OF THE N-TERMINAL HIS TAG OR OF RESIDUE 36 IN CHAINS A-H, AND OF RESIDUES A 435- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE IS INSUFFICIENT DENSITY TO ALLOW RELIABLE MODELLING OF THE N-TERMINAL HIS TAG OR OF RESIDUE 36 IN CHAINS A-H, AND OF RESIDUES A 435-436, B 434-444, C 441-443, D 441-445, E 441-446, F 435-448, G 440-447, H 434-441 AND H 445-448.
RfactorNum. reflection% reflectionSelection details
Rfree0.21403 32844 5 %RANDOM
Rwork0.19689 ---
obs0.19777 650665 94.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.339 Å2
Baniso -1Baniso -2Baniso -3
1-9.47 Å21.63 Å2-0.25 Å2
2---5.97 Å2-1.75 Å2
3----3.5 Å2
Refinement stepCycle: LAST / Resolution: 1.6→81.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33169 0 125 1636 34930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01934511
X-RAY DIFFRACTIONr_bond_other_d0.0030.0231941
X-RAY DIFFRACTIONr_angle_refined_deg1.9271.95147093
X-RAY DIFFRACTIONr_angle_other_deg1.351373287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.14954310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28224.2941621
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54614.8965384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.53315197
X-RAY DIFFRACTIONr_chiral_restr0.1160.25091
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02139778
X-RAY DIFFRACTIONr_gen_planes_other0.0010.028139
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_it2.0182.38917127
X-RAY DIFFRACTIONr_mcbond_other2.0172.38917125
X-RAY DIFFRACTIONr_mcangle_it2.5383.5921423
X-RAY DIFFRACTIONr_mcangle_other2.5383.5921424
X-RAY DIFFRACTIONr_scbond_it2.272.50317384
X-RAY DIFFRACTIONr_scbond_other2.2692.50317385
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0593.69925654
X-RAY DIFFRACTIONr_long_range_B_refined3.89419.46340477
X-RAY DIFFRACTIONr_long_range_B_other3.89419.46340478
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.635 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.558 1965 -
Rwork0.507 38933 -
obs--80.26 %

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