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- PDB-4fnt: Crystal structure of GH36 alpha-galactosidase AgaA A355E D548N fr... -

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Basic information

Entry
Database: PDB / ID: 4fnt
TitleCrystal structure of GH36 alpha-galactosidase AgaA A355E D548N from Geobacillus stearothermophilus in complex with raffinose
ComponentsAlpha-galactosidase AgaA
KeywordsHYDROLASE / Glycoside Hydrolase
Function / homology
Function and homology information


stachyose metabolic process / raffinose catabolic process / alpha-galactosidase / alpha-galactosidase activity / protein homotetramerization
Similarity search - Function
alpha-galactosidase from lactobacil brevis / Glycosyl hydrolase family 36, N-terminal / Glycosyl hydrolase family 36, C-terminal / Alpha-galactosidase, N-terminal domain superfamily / Glycosyl hydrolase family 36 C-terminal domain / Glycosyl hydrolase family 36 N-terminal domain / Glycoside hydrolase family 36 / Melibiase / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. ...alpha-galactosidase from lactobacil brevis / Glycosyl hydrolase family 36, N-terminal / Glycosyl hydrolase family 36, C-terminal / Alpha-galactosidase, N-terminal domain superfamily / Glycosyl hydrolase family 36 C-terminal domain / Glycosyl hydrolase family 36 N-terminal domain / Glycoside hydrolase family 36 / Melibiase / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. / Beta-galactosidase; Chain A, domain 5 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Distorted Sandwich / 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
raffinose / Alpha-galactosidase AgaA
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMerceron, R. / Foucault, M. / Haser, R. / Mattes, R. / Watzlawick, H. / Gouet, P.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: The molecular mechanism of the thermostable alpha-galactosidases AgaA and AgaB explained by X-ray crystallography and mutational studies
Authors: Merceron, R. / Foucault, M. / Haser, R. / Mattes, R. / Watzlawick, H. / Gouet, P.
History
DepositionJun 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_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.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-galactosidase AgaA
B: Alpha-galactosidase AgaA
C: Alpha-galactosidase AgaA
D: Alpha-galactosidase AgaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,8457
Polymers333,3324
Non-polymers1,5133
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23880 Å2
ΔGint-54 kcal/mol
Surface area83600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.680, 149.680, 234.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Alpha-galactosidase AgaA


Mass: 83332.891 Da / Num. of mol.: 4 / Mutation: A355E, D548N, M704V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: agaA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ALJ4, alpha-galactosidase
#2: Polysaccharide alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose-(1-2)-beta-D-fructofuranose / raffinose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: raffinose
DescriptorTypeProgram
DGalpa1-6DGlcpa1-2DFrufbGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[ha122h-2b_2-5][a2122h-1a_1-5][a2112h-1a_1-5]/1-2-3/a2-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{[(6+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 45.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 20% polyethylene glycol 3350, 0.2M potassium acetate, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2011
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 93989 / Num. obs: 92575 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 52.3 Å2 / Rsym value: 0.067 / Net I/σ(I): 12.22
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.8 / % possible all: 99.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XSCALEdata scaling
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→19.887 Å / SU ML: 0.3 / σ(F): 1.99 / Phase error: 22.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2212 4628 5 %
Rwork0.1696 --
obs0.1722 92571 98.76 %
all-92570 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.6173 Å20 Å2-0 Å2
2--1.6173 Å2-0 Å2
3----3.2346 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23160 0 102 357 23619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323856
X-RAY DIFFRACTIONf_angle_d0.74232362
X-RAY DIFFRACTIONf_dihedral_angle_d14.2668943
X-RAY DIFFRACTIONf_chiral_restr0.0523375
X-RAY DIFFRACTIONf_plane_restr0.0034224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.62950.30631550.21022957X-RAY DIFFRACTION100
2.6295-2.66040.28941520.2212883X-RAY DIFFRACTION100
2.6604-2.69270.30451550.21512932X-RAY DIFFRACTION100
2.6927-2.72670.29481550.21462946X-RAY DIFFRACTION100
2.7267-2.76250.28221540.20882932X-RAY DIFFRACTION100
2.7625-2.80030.26011530.20282906X-RAY DIFFRACTION100
2.8003-2.84020.3031550.19672943X-RAY DIFFRACTION100
2.8402-2.88240.24821540.19742926X-RAY DIFFRACTION99
2.8824-2.92730.26281530.19542913X-RAY DIFFRACTION99
2.9273-2.97520.30981500.21082856X-RAY DIFFRACTION98
2.9752-3.02630.29911530.212894X-RAY DIFFRACTION98
3.0263-3.08110.23981530.19782914X-RAY DIFFRACTION100
3.0811-3.14020.27731550.20072950X-RAY DIFFRACTION100
3.1402-3.2040.24121560.19862959X-RAY DIFFRACTION100
3.204-3.27340.25611550.20122952X-RAY DIFFRACTION100
3.2734-3.34920.27741540.1972925X-RAY DIFFRACTION100
3.3492-3.43250.22861550.19322937X-RAY DIFFRACTION99
3.4325-3.52480.29761530.18822910X-RAY DIFFRACTION99
3.5248-3.62790.25121530.17922914X-RAY DIFFRACTION98
3.6279-3.74430.21991530.16762893X-RAY DIFFRACTION98
3.7443-3.87720.2031510.16372870X-RAY DIFFRACTION97
3.8772-4.03120.21691510.15972873X-RAY DIFFRACTION96
4.0312-4.2130.18041550.14552939X-RAY DIFFRACTION99
4.213-4.43280.17221550.13342950X-RAY DIFFRACTION99
4.4328-4.70710.15081550.12782953X-RAY DIFFRACTION98
4.7071-5.0650.1691550.13332937X-RAY DIFFRACTION98
5.065-5.56450.20041530.15112905X-RAY DIFFRACTION97
5.5645-6.34670.22731540.16752927X-RAY DIFFRACTION97
6.3467-7.91150.18761610.16743052X-RAY DIFFRACTION99
7.9115-19.88760.18231620.14413095X-RAY DIFFRACTION98

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