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- PDB-7exj: Crystal structure of alkaline alpha-galctosidase D383A mutant fro... -

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Basic information

Entry
Database: PDB / ID: 7exj
TitleCrystal structure of alkaline alpha-galctosidase D383A mutant from Arabidopsis thaliana complexed with Raffinose
ComponentsProbable galactinol--sucrose galactosyltransferase 6
KeywordsTRANSFERASE / Alkaline alpha-galactosidase / HYDROLASE
Function / homology
Function and homology information


galactinol-sucrose galactosyltransferase / galactinol-sucrose galactosyltransferase activity
Similarity search - Function
Glycosyl hydrolases 36 / Raffinose synthase or seed imbibition protein Sip1 / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
raffinose / Probable galactinol--sucrose galactosyltransferase 6
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.47 Å
AuthorsChuankhayan, P. / Guan, H.H. / Lin, C.C. / Chen, N.C. / Huang, Y.C. / Yoshimura, M. / Nakagawa, A. / Lee, R.H. / Chen, C.J.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structural insight into the hydrolase and synthase activities of an alkaline alpha-galactosidase from Arabidopsis from complexes with substrate/product.
Authors: Chuankhayan, P. / Lee, R.H. / Guan, H.H. / Lin, C.C. / Chen, N.C. / Huang, Y.C. / Yoshimura, M. / Nakagawa, A. / Chen, C.J.
History
DepositionMay 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: 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
B: Probable galactinol--sucrose galactosyltransferase 6
A: Probable galactinol--sucrose galactosyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,4184
Polymers166,4092
Non-polymers1,0092
Water28816
1
B: Probable galactinol--sucrose galactosyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7092
Polymers83,2041
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint12 kcal/mol
Surface area25730 Å2
MethodPISA
2
A: Probable galactinol--sucrose galactosyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7092
Polymers83,2041
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint9 kcal/mol
Surface area25740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.603, 103.301, 181.436
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable galactinol--sucrose galactosyltransferase 6 / Protein DARK INDUCIBLE 10 / Raffinose synthase 6


Mass: 83204.406 Da / Num. of mol.: 2 / Mutation: D383A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RFS6, DIN10, RS6, At5g20250, F5O24.140 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8RX87, galactinol-sucrose galactosyltransferase
#2: Polysaccharide alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose-(1-2)-beta-D-fructofuranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: raffinose
DescriptorTypeProgram
DGalpa1-6DGlcpa1-2DFrufbGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[ha122h-2b_2-5][a2122h-1a_1-5][a2112h-1a_1-5]/1-2-3/a2-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][b-D-Tagf]{[(2+1)][b-L-Idop]{[(6+1)][a-D-Altp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 291.5 K / Method: microbatch / pH: 7.8 / Details: Tris, PEG 2000, PGA

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.47→30 Å / Num. obs: 118862 / % possible obs: 98.5 % / Redundancy: 3.116 % / Biso Wilson estimate: 67.722 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.074 / Χ2: 1.254 / Net I/σ(I): 10.56 / Num. measured all: 370410
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.47-2.623.2550.5011.786113019449187830.8120.60196.6
2.62-2.83.2280.3043.025868518216181780.9220.36599.8
2.8-3.023.1590.1745.165352417023169440.9740.2199.5
3.02-3.33.0060.1088.434648015643154600.9870.13298.8
3.3-3.692.9030.0713.464040614179139170.9920.08698.2
3.69-4.253.1640.05718.93895012482123110.9940.06898.6
4.25-5.183.1020.04922.153241810638104500.9940.0698.2
5.18-7.222.9250.04421.9323686822280980.9950.05398.5
7.22-303.2050.03725.3615131482047210.9970.04497.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EXG

7exg


Resolution: 2.47→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / SU B: 12.538 / SU ML: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.427 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 3170 5.1 %RANDOM
Rwork0.1905 ---
obs0.1935 59571 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 167.37 Å2 / Biso mean: 71.143 Å2 / Biso min: 35.44 Å2
Baniso -1Baniso -2Baniso -3
1-6.08 Å20 Å20 Å2
2---2.67 Å20 Å2
3----3.41 Å2
Refinement stepCycle: final / Resolution: 2.47→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11240 0 68 16 11324
Biso mean--73.42 56.16 -
Num. residues----1436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01911580
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210870
X-RAY DIFFRACTIONr_angle_refined_deg1.7161.95515694
X-RAY DIFFRACTIONr_angle_other_deg1.02325042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.16351430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10123.711512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.979151936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0121570
X-RAY DIFFRACTIONr_chiral_restr0.0980.21730
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02113014
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022676
LS refinement shellResolution: 2.47→2.534 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 215 -
Rwork0.386 4070 -
all-4285 -
obs--93.58 %

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