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

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Basic information

Entry
Database: PDB / ID: 6tbi
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-N8V / Beta-galactosidase, putative, bgl35A
Similarity search - Component
Biological speciesCellvibrio japonicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 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)501,19371
Polymers497,0168
Non-polymers4,17763
Water92,0035107
1
A: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5657
Polymers62,1271
Non-polymers4386
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6248
Polymers62,1271
Non-polymers4977
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5657
Polymers62,1271
Non-polymers4386
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,67010
Polymers62,1271
Non-polymers5439
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,78912
Polymers62,1271
Non-polymers66211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6248
Polymers62,1271
Non-polymers4977
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,76611
Polymers62,1271
Non-polymers63910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Beta-galactosidase, putative, bgl35A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5888
Polymers62,1271
Non-polymers4617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.120, 115.910, 116.103
Angle α, β, γ (deg.)90.200, 89.960, 90.080
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 (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.: 38 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-N8V / (1S,2S,3S,6R)-4-(hydroxymethyl)-6-(octylamino)cyclohex-4-ene-1,2,3-triol


Mass: 287.395 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C15H29NO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5107 / 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: 54.17 %
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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 2M / 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: 1.46→116.1 Å / Num. obs: 865389 / % possible obs: 96.4 % / Redundancy: 3.4 % / CC1/2: 0.996 / Net I/σ(I): 9.6
Reflection shellResolution: 1.46→1.48 Å / Num. unique obs: 41941 / CC1/2: 0.662

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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: 1.46→116.1 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.651 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.057
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY THE HYDROCARBON TAILS OF THE LIGAND MOLECULES ARE EITHER MODELLED WITH LOWERED OCCUPANCY ATOMS OR WITHOUT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY THE HYDROCARBON TAILS OF THE LIGAND MOLECULES ARE EITHER MODELLED WITH LOWERED OCCUPANCY ATOMS OR WITHOUT SOME ATOMS. THE LOOPS 433-447 HAVE BEEN MODELLED AT REDUCED OCCUPANCY OR WITH GAPS IN SOME OF THE MOLECULES.
RfactorNum. reflection% reflectionSelection details
Rfree0.1718 43369 5 %RANDOM
Rwork0.1259 ---
obs0.1282 821933 96.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 119.37 Å2 / Biso mean: 22.723 Å2 / Biso min: 12.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.63 Å2-0.4 Å2
2---1.36 Å2-0.61 Å2
3---1.05 Å2
Refinement stepCycle: final / Resolution: 1.46→116.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33818 0 256 5125 39199
Biso mean--25.17 37.25 -
Num. residues----4304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01335887
X-RAY DIFFRACTIONr_bond_other_d0.0020.01732218
X-RAY DIFFRACTIONr_angle_refined_deg1.9791.6548957
X-RAY DIFFRACTIONr_angle_other_deg1.6081.58374769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2554493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44922.8591896
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.998155611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.00515203
X-RAY DIFFRACTIONr_chiral_restr0.1150.24500
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0241151
X-RAY DIFFRACTIONr_gen_planes_other0.0030.027698
X-RAY DIFFRACTIONr_rigid_bond_restr5.156368105
LS refinement shellResolution: 1.46→1.498 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 3093 -
Rwork0.222 59345 -
all-62438 -
obs--93.97 %

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