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

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Basic information

Entry
Database: PDB / ID: 6lck
TitleTtGalA, alpha-galactosidase from Thermus thermophilus in complex with p-nitrophenyl alpha-D-galactopyranoside (alpha-NPG)
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 / 4-nitrophenyl alpha-D-galactopyranoside / Alpha-galactosidase
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 1.1Jul 29, 2020Group: Data collection / Derived calculations / Category: chem_comp / struct_site / struct_site_gen / Item: _chem_comp.mon_nstd_flag / _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)162,8636
Polymers161,9593
Non-polymers9043
Water0
1
B: Alpha-galactosidase
C: Alpha-galactosidase
hetero molecules

B: Alpha-galactosidase
C: Alpha-galactosidase
hetero molecules

A: Alpha-galactosidase
hetero molecules

A: Alpha-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)325,72512
Polymers323,9186
Non-polymers1,8076
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
crystal symmetry operation5_445x-1/2,y-1/2,z1
crystal symmetry operation7_544-x+1/2,y-1/2,-z-1/21
Unit cell
Length a, b, c (Å)118.631, 205.288, 163.898
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: Sugar ChemComp-9PG / 4-nitrophenyl alpha-D-galactopyranoside / 4-nitrophenyl alpha-D-galactoside / 4-nitrophenyl D-galactoside / 4-nitrophenyl galactoside


Type: D-saccharide / Mass: 301.249 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H15NO8 / Feature type: SUBJECT OF INVESTIGATION
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: 3.08 Å3/Da / Density % sol: 60.07 %
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: Jul 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.85→30 Å / Num. obs: 46936 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 47.39 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.9
Reflection shellResolution: 2.85→2.95 Å / Rmerge(I) obs: 0.505 / Num. unique obs: 4617

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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: 2.85→28.06 Å / SU ML: 0.3067 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4079
RfactorNum. reflection% reflection
Rfree0.2224 2010 4.29 %
Rwork0.1736 --
obs0.1757 46892 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.38 Å2
Refinement stepCycle: LAST / Resolution: 2.85→28.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11487 0 63 0 11550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009211919
X-RAY DIFFRACTIONf_angle_d1.058116224
X-RAY DIFFRACTIONf_chiral_restr0.05251626
X-RAY DIFFRACTIONf_plane_restr0.00682142
X-RAY DIFFRACTIONf_dihedral_angle_d3.74016891
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.920.29171410.2173109X-RAY DIFFRACTION99.09
2.92-30.30851380.22283168X-RAY DIFFRACTION100
3-3.090.28651390.223166X-RAY DIFFRACTION99.94
3.09-3.190.27351470.20453208X-RAY DIFFRACTION99.97
3.19-3.30.28481430.20113184X-RAY DIFFRACTION100
3.3-3.430.27371420.19943195X-RAY DIFFRACTION100
3.43-3.590.25251370.19193173X-RAY DIFFRACTION99.97
3.59-3.780.21951470.17673192X-RAY DIFFRACTION100
3.78-4.010.22711430.16563194X-RAY DIFFRACTION100
4.01-4.320.17911440.1523218X-RAY DIFFRACTION100
4.32-4.760.19081480.14193224X-RAY DIFFRACTION100
4.76-5.440.16931480.15063237X-RAY DIFFRACTION100
5.44-6.840.23551410.17773260X-RAY DIFFRACTION100
6.84-28.060.17721520.15353354X-RAY DIFFRACTION99.26

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