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- PDB-6lcj: TtGalA, alpha-galactosidase from Thermus thermopilus in apo form -

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Basic information

Entry
Database: PDB / ID: 6lcj
TitleTtGalA, alpha-galactosidase from Thermus thermopilus in apo form
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: 2.5 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 fromThermus 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 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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: Alpha-galactosidase
B: Alpha-galactosidase
C: Alpha-galactosidase
D: Alpha-galactosidase
E: Alpha-galactosidase
F: Alpha-galactosidase


Theoretical massNumber of molelcules
Total (without water)323,9186
Polymers323,9186
Non-polymers00
Water14,844824
1
B: Alpha-galactosidase
D: Alpha-galactosidase
E: Alpha-galactosidase

A: Alpha-galactosidase

C: Alpha-galactosidase

F: Alpha-galactosidase


Theoretical massNumber of molelcules
Total (without water)323,9186
Polymers323,9186
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
crystal symmetry operation2_546-x,y-1/2,-z+11
Unit cell
Length a, b, c (Å)118.435, 163.496, 118.650
Angle α, β, γ (deg.)90.000, 119.920, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Alpha-galactosidase


Mass: 53986.309 Da / Num. of mol.: 6
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 824 / Source method: isolated from a natural source / Formula: H2O

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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: 3.07 Å3/Da / Density % sol: 59.98 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium acetate pH 4.4, 0.02M CaCl2, 30% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.5→34.28 Å / Num. obs: 133881 / % possible obs: 99.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 34.14 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 13.8
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.49 / Num. unique obs: 13343

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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: 1ZY9

1zy9


Resolution: 2.5→34.28 Å / SU ML: 0.2541 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.1716
RfactorNum. reflection% reflection
Rfree0.2017 2011 1.5 %
Rwork0.1645 --
obs0.1651 133787 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.6 Å2
Refinement stepCycle: LAST / Resolution: 2.5→34.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22634 0 0 824 23458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007823356
X-RAY DIFFRACTIONf_angle_d0.916931787
X-RAY DIFFRACTIONf_chiral_restr0.04943176
X-RAY DIFFRACTIONf_plane_restr0.00624207
X-RAY DIFFRACTIONf_dihedral_angle_d3.213713567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.570.27241410.22779211X-RAY DIFFRACTION97.65
2.57-2.640.26971410.21369430X-RAY DIFFRACTION99.85
2.64-2.710.29361470.20799309X-RAY DIFFRACTION99.97
2.71-2.80.24161510.19559441X-RAY DIFFRACTION99.99
2.8-2.90.2261360.18799452X-RAY DIFFRACTION99.99
2.9-3.020.2181450.18039432X-RAY DIFFRACTION100
3.02-3.160.23321330.17589413X-RAY DIFFRACTION99.99
3.16-3.320.2171440.16699415X-RAY DIFFRACTION99.99
3.32-3.530.19961440.16169412X-RAY DIFFRACTION99.98
3.53-3.80.20891450.15379477X-RAY DIFFRACTION99.98
3.8-4.180.16581520.13949393X-RAY DIFFRACTION99.96
4.18-4.790.14561430.13219470X-RAY DIFFRACTION99.93
4.79-6.030.16931400.16029475X-RAY DIFFRACTION99.8
6.03-34.280.20351490.15819446X-RAY DIFFRACTION98.64

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