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- PDB-7exg: Crystal structure of D383A mutant from Arabidopsis thaliana compl... -

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Basic information

Entry
Database: PDB / ID: 7exg
TitleCrystal structure of D383A mutant from Arabidopsis thaliana complexed with Galactose.
ComponentsProbable galactinol--sucrose galactosyltransferase 6
KeywordsTRANSFERASE / Alkaline alpha-galactosidase / HYDROLASE
Function / homologygalactinol-sucrose galactosyltransferase / galactinol-sucrose galactosyltransferase activity / Glycosyl hydrolases 36 / Raffinose synthase or seed imbibition protein Sip1 / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / beta-D-galactopyranose / Probable galactinol--sucrose galactosyltransferase 6
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 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

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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)166,7694
Polymers166,4092
Non-polymers3602
Water10,431579
1
B: Probable galactinol--sucrose galactosyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3852
Polymers83,2041
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint3 kcal/mol
Surface area25800 Å2
MethodPISA
2
A: Probable galactinol--sucrose galactosyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3852
Polymers83,2041
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint2 kcal/mol
Surface area25750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.030, 103.736, 182.694
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: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / 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: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 291.15 K / Method: microbatch / pH: 7.8 / Details: 0.1 M Tris, PEG 2000, 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 MX-300 / Detector: CCD / Date: Mar 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 111655 / % possible obs: 99.3 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.032 / Rrim(I) all: 0.082 / Χ2: 1.056 / Net I/σ(I): 10.1 / Num. measured all: 714794
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.125.80.554105890.9060.2410.6060.7695.4
2.12-2.216.30.395110590.9550.1680.430.77299.4
2.21-2.316.60.308111410.970.1290.3340.811100
2.31-2.436.70.21111190.9840.0880.2280.857100
2.43-2.586.60.152112010.9890.0640.1650.959100
2.58-2.786.60.111111760.9930.0470.121.136100
2.78-3.066.60.085112260.9950.0360.0931.318100
3.06-3.56.60.073112800.9950.030.0791.41999.9
3.5-4.416.30.07112750.9950.0290.0761.32499.4
4.41-305.80.053115890.9960.0230.0581.15798.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0049refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EXF

7exf


Resolution: 2.05→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.686 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2352 5259 5 %RANDOM
Rwork0.1838 ---
obs0.1864 99082 92.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.11 Å2 / Biso mean: 31.161 Å2 / Biso min: 9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11220 0 22 579 11821
Biso mean--20.51 31.84 -
Num. residues----1432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01911509
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210862
X-RAY DIFFRACTIONr_angle_refined_deg2.0071.9515585
X-RAY DIFFRACTIONr_angle_other_deg0.966325024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.83551426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.37423.711512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.6151936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8171570
X-RAY DIFFRACTIONr_chiral_restr0.1360.21706
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02112984
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022674
LS refinement shellResolution: 2.051→2.104 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 258 -
Rwork0.239 4876 -
all-5134 -
obs--62.88 %

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