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

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Basic information

Entry
Database: PDB / ID: 6tbf
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
ACETATE ION / Chem-N0T / 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 1.2Mar 2, 2022Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)500,85165
Polymers497,0168
Non-polymers3,83457
Water82,5094580
1
A: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5537
Polymers62,1271
Non-polymers4266
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5075
Polymers62,1271
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4946
Polymers62,1271
Non-polymers3675
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,69410
Polymers62,1271
Non-polymers5679
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,65810
Polymers62,1271
Non-polymers5319
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6128
Polymers62,1271
Non-polymers4857
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,75411
Polymers62,1271
Non-polymers62710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5768
Polymers62,1271
Non-polymers4497
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.423, 115.626, 115.942
Angle α, β, γ (deg.)90.350, 90.020, 90.160
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.: 35 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-N0T / (1~{S},2~{S},3~{S},4~{R},5~{R})-4-(hydroxymethyl)-5-(octylamino)cyclopentane-1,2,3-triol


Mass: 275.384 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H29NO4 / 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.: 4580 / 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: 2.68 Å3/Da / Density % sol: 54.13 %
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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→115.94 Å / Num. obs: 798809 / % possible obs: 96.6 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.1
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 38828 / CC1/2: 0.693

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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: 1.5→115.94 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.848 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.063
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY THERE IS UNMODELLED DENSITY BETWEEN THE SIDE CHAIN OF TRP480 AND THE HYDROCARBON CHAIN OF THE LIGAND IN SOME ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY THERE IS UNMODELLED DENSITY BETWEEN THE SIDE CHAIN OF TRP480 AND THE HYDROCARBON CHAIN OF THE LIGAND IN SOME OF THE MOLECULES THE LOOPS BETWEEN THR433 AND LYS448 HAVE BEEN MODELLED AT REDUCED OCCUPANCY OR WITH CHAIN BREAKS WHERE RESIDUES COULD NOT BE PLACED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1776 40201 5 %RANDOM
Rwork0.1275 ---
obs0.13 758576 96.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 154.4 Å2 / Biso mean: 23.913 Å2 / Biso min: 12.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.81 Å20.63 Å2
2--0.26 Å2-0.54 Å2
3----0.99 Å2
Refinement stepCycle: final / Resolution: 1.5→115.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33861 0 243 4590 38694
Biso mean--24.83 36.81 -
Num. residues----4315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01335816
X-RAY DIFFRACTIONr_bond_other_d0.0020.01732177
X-RAY DIFFRACTIONr_angle_refined_deg1.9681.65148848
X-RAY DIFFRACTIONr_angle_other_deg1.6211.58474669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.14554481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30922.8481896
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.329155587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.06715205
X-RAY DIFFRACTIONr_chiral_restr0.1170.24508
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0240952
X-RAY DIFFRACTIONr_gen_planes_other0.0020.027669
X-RAY DIFFRACTIONr_rigid_bond_restr4.918367993
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 2871 -
Rwork0.211 54957 -
all-57828 -
obs--94.4 %

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