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- PDB-7exq: Crystal structure of alkaline alpha-galactosidase D383A mutant fr... -

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Basic information

Entry
Database: PDB / ID: 7exq
TitleCrystal structure of alkaline alpha-galactosidase D383A mutant from Arabidopsis thaliana complexed with product-galactose and sucrose.
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
sucrose / beta-D-galactopyranose / Probable galactinol--sucrose galactosyltransferase 6
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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 28, 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)167,4546
Polymers166,4092
Non-polymers1,0454
Water7,494416
1
B: Probable galactinol--sucrose galactosyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7273
Polymers83,2041
Non-polymers5222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area26000 Å2
MethodPISA
2
A: Probable galactinol--sucrose galactosyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7273
Polymers83,2041
Non-polymers5222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint6 kcal/mol
Surface area26150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.710, 104.101, 182.420
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 beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 291.5 K / Method: microbatch / Details: Tris, PEG2000, PGA

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 92281 / % possible obs: 97.2 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.036 / Rrim(I) all: 0.085 / Χ2: 0.884 / Net I/σ(I): 8.9 / Num. measured all: 500553
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.285.60.71793810.880.3270.7890.817100
2.28-2.375.80.69994000.9280.3140.7690.813100
2.37-2.485.80.43993700.9590.1970.4830.835100
2.48-2.615.80.3194130.9770.1390.3410.833100
2.61-2.775.70.21394080.9860.0960.2340.87699.9
2.77-2.995.70.1494180.9920.0640.1550.96399.7
2.99-3.295.60.08493860.9960.0390.0930.96699
3.29-3.765.20.05391870.9970.0250.0591.00496.4
3.76-4.734.20.0481410.9970.0220.0461.06385
4.73-304.70.02791770.9980.0140.0310.72892.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EXG

7exg


Resolution: 2.2→29.88 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.067 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2547 4303 5 %RANDOM
Rwork0.1925 ---
obs0.1955 82212 91.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.51 Å2 / Biso mean: 40.111 Å2 / Biso min: 16.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.2→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11242 0 70 416 11728
Biso mean--55.24 37.57 -
Num. residues----1436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01911582
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210898
X-RAY DIFFRACTIONr_angle_refined_deg1.9371.95515694
X-RAY DIFFRACTIONr_angle_other_deg1.089325120
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.35651430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30123.711512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.814151938
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5371570
X-RAY DIFFRACTIONr_chiral_restr0.1520.21730
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02113014
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022676
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 202 -
Rwork0.297 3726 -
all-3928 -
obs--56.72 %

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