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- PDB-6lcl: TtGalA, alpha-galactosidase from Thermus thermophilus in complex ... -

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Basic information

Entry
Database: PDB / ID: 6lcl
TitleTtGalA, alpha-galactosidase from Thermus thermophilus in complex with stachyose
ComponentsAlpha-galactosidase
KeywordsHYDROLASE / alpha-galactosidase / hexamer assembly / substrate specificity / thermostable / stachyose
Function / homologyGlycoside hydrolase family 36 / Melibiase / alpha-galactosidase activity / carbohydrate catabolic process / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / Alpha-galactosidase
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsChen, S.C. / Hsu, C.H.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (Taiwan)108-2628-B-002-013 Taiwan
Ministry of Science and Technology (Taiwan)108-2113-M-002-011 Taiwan
CitationJournal: J.Agric.Food Chem. / Year: 2020
Title: Crystal Structure of alpha-Galactosidase from Thermus thermophilus : Insight into Hexamer Assembly and Substrate Specificity.
Authors: Chen, S.C. / Wu, S.P. / Chang, Y.Y. / Hwang, T.S. / Lee, T.H. / Hsu, C.H.
History
DepositionNov 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-galactosidase
C: Alpha-galactosidase
E: Alpha-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,9866
Polymers161,9593
Non-polymers1,0273
Water00
1
C: Alpha-galactosidase
hetero molecules

C: Alpha-galactosidase
hetero molecules

A: Alpha-galactosidase
hetero molecules

E: Alpha-galactosidase
hetero molecules

A: Alpha-galactosidase
hetero molecules

E: Alpha-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)325,97212
Polymers323,9186
Non-polymers2,0546
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_754-x+2,y,-z-1/21
crystal symmetry operation5_545x+1/2,y-1/2,z1
crystal symmetry operation6_644-x+3/2,-y-1/2,z-1/21
crystal symmetry operation7_644-x+3/2,y-1/2,-z-1/21
crystal symmetry operation8_545x+1/2,-y-1/2,-z1
Unit cell
Length a, b, c (Å)118.446, 205.010, 163.392
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Alpha-galactosidase / GalA


Mass: 53986.309 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Gene: TTHB115 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53W51
#2: Polysaccharide alpha-D-galactopyranose-(1-6)-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-6DGalpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2112h-1a_1-5]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Galp]{[(6+1)][a-D-Galp]{}}LINUCSPDB-CARE
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: 3.06 Å3/Da / Density % sol: 59.83 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: 0.1M CAPSO pH 9.2, 0.2M Li2SO4, 10% PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 32852 / % possible obs: 99.3 % / Redundancy: 7 % / Biso Wilson estimate: 62.78 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 19.2
Reflection shellResolution: 3.2→3.31 Å / Rmerge(I) obs: 0.504 / Num. unique obs: 3187

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo structure

Resolution: 3.2→25.22 Å / SU ML: 0.3173 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.4208
RfactorNum. reflection% reflection
Rfree0.2138 1994 6.08 %
Rwork0.1531 --
obs0.1568 32822 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 53.87 Å2
Refinement stepCycle: LAST / Resolution: 3.2→25.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11287 0 66 0 11353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009711716
X-RAY DIFFRACTIONf_angle_d1.085915949
X-RAY DIFFRACTIONf_chiral_restr0.05571609
X-RAY DIFFRACTIONf_plane_restr0.00722098
X-RAY DIFFRACTIONf_dihedral_angle_d2.99136762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.280.29431250.19861971X-RAY DIFFRACTION90.78
3.28-3.360.28241430.17932195X-RAY DIFFRACTION99.03
3.36-3.460.24131420.17642156X-RAY DIFFRACTION99.14
3.46-3.580.24281440.17032186X-RAY DIFFRACTION99.7
3.58-3.70.24461410.16672212X-RAY DIFFRACTION99.87
3.7-3.850.25331400.16042192X-RAY DIFFRACTION99.91
3.85-4.020.22541480.15132212X-RAY DIFFRACTION99.83
4.02-4.240.19161470.14222217X-RAY DIFFRACTION99.66
4.24-4.50.1941440.12862190X-RAY DIFFRACTION99.7
4.5-4.850.18171410.13522208X-RAY DIFFRACTION99.37
4.85-5.330.18941400.14052246X-RAY DIFFRACTION99.75
5.33-6.090.22081470.1672248X-RAY DIFFRACTION100
6.09-7.640.21251410.16412266X-RAY DIFFRACTION99.96
7.64-25.220.17931510.13952329X-RAY DIFFRACTION98.88

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