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

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Basic information

Entry
Database: PDB / ID: 6tbk
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-N0Q / Beta-galactosidase, putative, bgl35A
Similarity search - Component
Biological speciesCellvibrio japonicus Ueda107 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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

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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)501,58948
Polymers497,0168
Non-polymers4,57340
Water45,0742502
1
A: 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
2
B: 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
3
C: 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
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)62,7227
Polymers62,1271
Non-polymers5956
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)62,7227
Polymers62,1271
Non-polymers5956
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6534
Polymers62,1271
Non-polymers5263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.952, 116.052, 115.576
Angle α, β, γ (deg.)89.840, 90.070, 89.980
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.: 32 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-N0Q / 5-(dimethylamino)-~{N}-[6-[(2~{R},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


Mass: 18.015 Da / Num. of mol.: 2502 / 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: 2.67 Å3/Da / Density % sol: 53.94 %
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: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→63.2 Å / Num. obs: 650269 / % possible obs: 95.8 % / Redundancy: 2.1 % / CC1/2: 0.995 / Net I/σ(I): 4.6
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 31475 / CC1/2: 0.678

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Processing

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

4d1i


Resolution: 1.6→63.2 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.835 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.085
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 AND D. THE HYDROCARBON TAILS OF THE LIGAND MOLECULES ARE EITHER MODELLED WITH LOWERED OCCUPANCY ATOMS OR WITHOUT SOME ATOMS. IN SOME OF THE MOLECULES THE LOOPS BETWEEN THR432 AND GLU449 HAVE BEEN MODELLED AT REDUCED OCCUPANCY OR WITH CHAIN BREAKS WHERE RESIDUES COULD NOT BE PLACED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2118 32511 5 %RANDOM
Rwork0.1519 ---
obs0.1549 617754 95.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 99.96 Å2 / Biso mean: 26.906 Å2 / Biso min: 13.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å2-0.04 Å2-1.4 Å2
2---1.16 Å2-0.02 Å2
3---0.94 Å2
Refinement stepCycle: final / Resolution: 1.6→63.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33342 0 157 2502 36001
Biso mean--27.71 33.61 -
Num. residues----4260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01334521
X-RAY DIFFRACTIONr_bond_other_d0.0110.01731031
X-RAY DIFFRACTIONr_angle_refined_deg1.9421.64947079
X-RAY DIFFRACTIONr_angle_other_deg1.6841.58271892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55154278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66522.8411816
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.993155310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.80615191
X-RAY DIFFRACTIONr_chiral_restr0.1040.24363
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0239110
X-RAY DIFFRACTIONr_gen_planes_other0.0060.027399
X-RAY DIFFRACTIONr_rigid_bond_restr7.169365540
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 2300 -
Rwork0.29 44671 -
all-46971 -
obs--93.51 %

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