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

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Basic information

Entry
Database: PDB / ID: 7exr
TitleCrystal structure of alkaline alpha-galactosidase D383A mutant from Arabidopsis thaliana complexed with Stachyose.
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
Probable galactinol--sucrose galactosyltransferase 6
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 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 2.0Oct 4, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_instance_feature / pdbx_molecule_features / pdbx_validate_chiral / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_branch_scheme.mon_id / _pdbx_branch_scheme.pdb_mon_id / _pdbx_entity_branch_descriptor.descriptor / _pdbx_entity_branch_link.comp_id_1 / _pdbx_entity_branch_link.comp_id_2 / _pdbx_entity_branch_list.comp_id / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: 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)167,7424
Polymers166,4092
Non-polymers1,3332
Water9,800544
1
B: Probable galactinol--sucrose galactosyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8712
Polymers83,2041
Non-polymers6671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Probable galactinol--sucrose galactosyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8712
Polymers83,2041
Non-polymers6671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.589, 103.749, 182.372
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-galactopyranose-(1-6)-alpha-D-glucopyranose-(1-2)-beta-D-fructofuranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-6DGalpa1-6DGlcpa1-2DFrufbGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[ha122h-2b_2-5][a2122h-1a_1-5][a2112h-1a_1-5]/1-2-3-3/a2-b1_b6-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{[(6+1)][a-D-Galp]{[(6+1)][a-D-Galp]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 2.77 Å3/Da / Density % sol: 55.64 %
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: NSRRC / Beamline: BL15A1 / Wavelength: 0.97 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 124558 / % possible obs: 99.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.04 / Rrim(I) all: 0.101 / Χ2: 1.366 / Net I/σ(I): 7.2 / Num. measured all: 785125
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.075.40.597122780.8550.2770.660.65799.5
2.07-2.156.10.488123310.9230.2140.5330.701100
2.15-2.256.40.395123510.9490.1690.430.788100
2.25-2.376.40.309123350.9660.1320.3370.845100
2.37-2.526.50.235123700.9770.10.2550.981100
2.52-2.716.50.178124160.9860.0760.1931.144100
2.71-2.996.60.127124300.9910.0540.1381.393100
2.99-3.426.60.086124850.9950.0360.0931.672100
3.42-4.316.50.067126120.9960.0290.0732.34100
4.31-3060.064129500.9950.0290.0712.96499.8

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Phasing

PhasingMethod: molecular replacement

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Processing

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

7exg


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.689 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2064 6172 5 %RANDOM
Rwork0.1672 ---
obs0.1692 118298 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 155.89 Å2 / Biso mean: 42.678 Å2 / Biso min: 22.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11240 0 90 544 11874
Biso mean--55.5 44.82 -
Num. residues----1436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01911603
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210931
X-RAY DIFFRACTIONr_angle_refined_deg2.011.95815729
X-RAY DIFFRACTIONr_angle_other_deg1.135325209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.72351430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38523.699511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05151936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6751570
X-RAY DIFFRACTIONr_chiral_restr0.1570.21741
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02113008
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022674
LS refinement shellResolution: 2.003→2.055 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 437 -
Rwork0.249 8363 -
all-8800 -
obs--97.06 %

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