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- PDB-6f4c: Nicotiana benthamiana alpha-galactosidase -

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Basic information

Entry
Database: PDB / ID: 6f4c
TitleNicotiana benthamiana alpha-galactosidase
Componentsalpha-galactosidase
KeywordsHYDROLASE / alpha-galactosidase Nicotiana benthamiana
Function / homology
Function and homology information


plant-type cell wall / alpha-galactosidase / alpha-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
Alpha galactosidase, C-terminal beta sandwich domain / Alpha galactosidase C-terminal beta sandwich domain / Alpha galactosidase A / Glycoside hydrolase, family 27 / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Aldolase class I / Aldolase-type TIM barrel ...Alpha galactosidase, C-terminal beta sandwich domain / Alpha galactosidase C-terminal beta sandwich domain / Alpha galactosidase A / Glycoside hydrolase, family 27 / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesNicotiana benthamiana (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKytidou, K. / Aerts, J.M.F.G. / Pannu, N.S.
Funding support Netherlands, 2items
OrganizationGrant numberCountry
European Research Council Netherlands
ZonMW Netherlands
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Nicotiana benthamianaalpha-galactosidase A1.1 can functionally complement human alpha-galactosidase A deficiency associated with Fabry disease.
Authors: Kytidou, K. / Beekwilder, J. / Artola, M. / van Meel, E. / Wilbers, R.H.P. / Moolenaar, G.F. / Goosen, N. / Ferraz, M.J. / Katzy, R. / Voskamp, P. / Florea, B.I. / Hokke, C.H. / Overkleeft, ...Authors: Kytidou, K. / Beekwilder, J. / Artola, M. / van Meel, E. / Wilbers, R.H.P. / Moolenaar, G.F. / Goosen, N. / Ferraz, M.J. / Katzy, R. / Voskamp, P. / Florea, B.I. / Hokke, C.H. / Overkleeft, H.S. / Schots, A. / Bosch, D. / Pannu, N. / Aerts, J.M.F.G.
History
DepositionNov 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: alpha-galactosidase


Theoretical massNumber of molelcules
Total (without water)39,9271
Polymers39,9271
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.037, 74.037, 133.307
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein alpha-galactosidase


Mass: 39927.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana benthamiana (plant) / Production host: Nicotiana benthamiana (plant) / References: UniProt: A0A384E148*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.2 M LiSO4 0.1 M BIS-TRIS 5.5 pH 25 %w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 7, 2016 / Details: CRL
RadiationMonochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.8→64.72 Å / Num. obs: 9569 / % possible obs: 98.8 % / Redundancy: 7.2 % / Net I/σ(I): 5.4
Reflection shellResolution: 2.8→64.72 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1uas

1uas


Resolution: 2.8→64.72 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.808 / SU B: 17.762 / SU ML: 0.344 / Cross valid method: THROUGHOUT / ESU R Free: 0.459 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28505 486 5.1 %RANDOM
Rwork0.21058 ---
obs0.21432 9060 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 3.809 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å2-0 Å2-0 Å2
2--0.5 Å2-0 Å2
3----1.01 Å2
Refinement stepCycle: 1 / Resolution: 2.8→64.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2799 0 0 63 2862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192865
X-RAY DIFFRACTIONr_bond_other_d0.0020.022517
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.9273885
X-RAY DIFFRACTIONr_angle_other_deg2.10235862
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3075362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.10624.733131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.85815473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2211515
X-RAY DIFFRACTIONr_chiral_restr0.0830.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023251
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02588
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1910.3911451
X-RAY DIFFRACTIONr_mcbond_other0.190.3911450
X-RAY DIFFRACTIONr_mcangle_it0.360.5861812
X-RAY DIFFRACTIONr_mcangle_other0.360.5871813
X-RAY DIFFRACTIONr_scbond_it0.1090.3861414
X-RAY DIFFRACTIONr_scbond_other0.1090.3871415
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.2160.5732074
X-RAY DIFFRACTIONr_long_range_B_refined1.2236.78812670
X-RAY DIFFRACTIONr_long_range_B_other1.2196.79312660
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 27 -
Rwork0.284 578 -
obs--85.82 %

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