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- PDB-6tbj: Structure of a beta galactosidase with inhibitor -

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Basic information

Entry
Database: PDB / ID: 6tbj
TitleStructure of a beta galactosidase with inhibitor
ComponentsBeta-galactosidase, putative, bgl35A
KeywordsHYDROLASE / beta galactosidase / inhibitor
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
Chem-N0W / Beta-galactosidase, putative, bgl35A
Similarity search - Component
Biological speciesCellvibrio japonicus Ueda107 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsOffen, W. / Davies, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/R001162/1 United Kingdom
CitationJournal: Molecules / Year: 2020
Title: Mechanistic Insights into the Chaperoning of Human Lysosomal-Galactosidase Activity: Highly Functionalized Aminocyclopentanes and C -5a-Substituted Derivatives of 4- epi -Isofagomine.
Authors: Weber, P. / Thonhofer, M. / Averill, S. / Davies, G.J. / Santana, A.G. / Muller, P. / Nasseri, S.A. / Offen, W.A. / Pabst, B.M. / Paschke, E. / Schalli, M. / Torvisco, A. / Tschernutter, M. ...Authors: Weber, P. / Thonhofer, M. / Averill, S. / Davies, G.J. / Santana, A.G. / Muller, P. / Nasseri, S.A. / Offen, W.A. / Pabst, B.M. / Paschke, E. / Schalli, M. / Torvisco, A. / Tschernutter, M. / Tysoe, C. / Windischhofer, W. / Withers, S.G. / Wolfsgruber, A. / Wrodnigg, T.M. / Stutz, A.E.
History
DepositionNov 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)501,47443
Polymers497,0168
Non-polymers4,45835
Water37,7412095
1
A: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6765
Polymers62,1271
Non-polymers5494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6303
Polymers62,1271
Non-polymers5032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6765
Polymers62,1271
Non-polymers5494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7227
Polymers62,1271
Non-polymers5956
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6996
Polymers62,1271
Non-polymers5725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6996
Polymers62,1271
Non-polymers5725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6765
Polymers62,1271
Non-polymers5494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6996
Polymers62,1271
Non-polymers5725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.416, 115.786, 116.186
Angle α, β, γ (deg.)89.930, 90.080, 89.990
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 predicted signal sequence and with N-terminal his 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.: 27 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-N0W / 5-(dimethylamino)-~{N}-[6-[(2~{S},3~{R},4~{S},5~{R})-3-(hydroxymethyl)-4,5-bis(oxidanyl)piperidin-2-yl]hexyl]naphthalene-1-sulfonamide


Mass: 479.633 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C24H37N3O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2095 / 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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: Sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2016
RadiationProtocol: 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, L10.582
11h,-k,-l20.048
11H, -L, K30.089
11H, L, -K40.281
ReflectionResolution: 1.5→63.21 Å / Num. obs: 793061 / % possible obs: 95.6 % / Redundancy: 1.8 % / CC1/2: 0.982 / Net I/σ(I): 4.9
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 38760 / CC1/2: 0.585

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D1I

4d1i


Resolution: 1.5→63.21 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.888 / SU ML: 0.017 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.014 / ESU R Free: 0.012
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY THE (DIMETHYLAMINO)NAPHTHALENE GROUPS OF THE LIGAND HAVE NOT BEEN MODELLED AS THERE IS INSUFFICIENT DENSITY, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY THE (DIMETHYLAMINO)NAPHTHALENE GROUPS OF THE LIGAND HAVE NOT BEEN MODELLED AS THERE IS INSUFFICIENT DENSITY, AND THE SULFONYL GROUP IS ONLY MODELLED IN THE ACTIVE SITES OF MOLECULES A, D AND F.IN SOME OF THE MOLECULES THE LOOPS BETWEEN THR432 AND GLN450 HAVE BEEN MODELLED AT REDUCED OCCUPANCY OR WITH CHAIN BREAKS WHERE RESIDUES COULD NOT BE PLACED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1644 40511 5.1 %RANDOM
Rwork0.1451 ---
obs0.1461 752547 94.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 60.93 Å2 / Biso mean: 20.036 Å2 / Biso min: 11.15 Å2
Baniso -1Baniso -2Baniso -3
1-3.83 Å2-0.22 Å21.72 Å2
2---4.61 Å23.39 Å2
3---0.78 Å2
Refinement stepCycle: final / Resolution: 1.5→63.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33088 0 160 2095 35343
Biso mean--21.67 26.22 -
Num. residues----4224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01334275
X-RAY DIFFRACTIONr_bond_other_d0.0010.01730871
X-RAY DIFFRACTIONr_angle_refined_deg1.8371.64946750
X-RAY DIFFRACTIONr_angle_other_deg1.5661.58271561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75254253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09922.9111807
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.917155296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.38815188
X-RAY DIFFRACTIONr_chiral_restr0.1020.24334
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0238839
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027313
X-RAY DIFFRACTIONr_rigid_bond_restr3.671365136
LS refinement shellResolution: 1.495→1.534 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.195 2419 -
Rwork0.13 47559 -
all-49978 -
obs--80.31 %

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