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- PDB-7exf: Crystal structure of wild-type from Arabidopsis thaliana complexe... -

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Basic information

Entry
Database: PDB / ID: 7exf
TitleCrystal structure of wild-type 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 / MAD / Resolution: 2.17 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.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)108-2311-B-213-001-MY3 Taiwan
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 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)166,8574
Polymers166,4972
Non-polymers3602
Water3,171176
1
B: Probable galactinol--sucrose galactosyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4292
Polymers83,2481
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Probable galactinol--sucrose galactosyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4292
Polymers83,2481
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.938, 103.644, 181.214
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: 83248.414 Da / Num. of mol.: 2
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.: 176 / 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: 54.06 %
Crystal growTemperature: 291.15 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: NSRRC / Beamline: TPS 05A / Wavelength: 0.972 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.17→30 Å / Num. obs: 95207 / % possible obs: 98.2 % / Redundancy: 6 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.036 / Rrim(I) all: 0.086 / Χ2: 1.05 / Net I/σ(I): 13.4 / Num. measured all: 568408
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.17-2.2560.77679880.8290.3380.8481.08983.7
2.25-2.346.60.61395990.9050.2590.6661.112100
2.34-2.446.60.43395950.9510.1830.4711.091100
2.44-2.576.60.31696110.9720.1340.3441.059100
2.57-2.736.50.22996450.9820.0980.2491.088100
2.73-2.946.20.16596260.990.0720.181.032100
2.94-3.245.90.1196830.9940.050.1211.054100
3.24-3.715.40.06997320.9970.0330.0760.982100
3.71-4.674.90.05397360.9970.0250.0590.93699.4
4.67-305.10.04499920.9980.020.0491.00698.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.17→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.764 / SU ML: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.234 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2669 4756 5 %RANDOM
Rwork0.2079 ---
obs0.2109 90033 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 147.63 Å2 / Biso mean: 60.976 Å2 / Biso min: 27.69 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2.17→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11251 0 24 176 11451
Biso mean--53 44.1 -
Num. residues----1436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01911538
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210884
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.9515627
X-RAY DIFFRACTIONr_angle_other_deg1.063325083
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.96251430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65823.735514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.504151938
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6061570
X-RAY DIFFRACTIONr_chiral_restr0.1120.21712
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02113021
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022677
LS refinement shellResolution: 2.17→2.226 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 317 -
Rwork0.32 6529 -
all-6846 -
obs--98.77 %

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