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- PDB-4fns: Crystal structure of GH36 alpha-galactosidase AgaA A355E from Geo... -

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Basic information

Entry
Database: PDB / ID: 4fns
TitleCrystal structure of GH36 alpha-galactosidase AgaA A355E from Geobacillus stearothermophilus in complex with 1-deoxygalactonojirimycin
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 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
Chem-DGJ / 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 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)334,68317
Polymers333,1994
Non-polymers1,48313
Water17,655980
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23700 Å2
ΔGint-55 kcal/mol
Surface area82710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.300, 150.300, 233.360
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: 83299.859 Da / Num. of mol.: 4 / Mutation: A355E, F518L, 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: Chemical
ChemComp-DGJ / (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol / 1-deoxygalactonojirimycin


Mass: 163.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: Galafold, medication*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 980 / 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: 46.14 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 20% PEG 3350, 0.2M Potassium nitrate, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.18 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 1, 2011
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 94216 / Num. obs: 91886 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Biso Wilson estimate: 32.6 Å2 / Rsym value: 0.072 / Net I/σ(I): 11.35
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3 / % possible all: 96.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3MI6

3mi6


Resolution: 2.6→49.197 Å / SU ML: 0.31 / σ(F): 1.99 / Phase error: 22.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 4596 5 %
Rwork0.1738 --
obs0.1767 91886 97.61 %
all-91886 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.8759 Å2-0 Å2-0 Å2
2--0.8759 Å2-0 Å2
3----1.7517 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23148 0 88 980 24216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223811
X-RAY DIFFRACTIONf_angle_d0.60932290
X-RAY DIFFRACTIONf_dihedral_angle_d10.9118765
X-RAY DIFFRACTIONf_chiral_restr0.0443392
X-RAY DIFFRACTIONf_plane_restr0.0024220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.62950.26581510.20652880X-RAY DIFFRACTION98
2.6295-2.66050.29631490.21732829X-RAY DIFFRACTION97
2.6605-2.69290.28421500.21812854X-RAY DIFFRACTION96
2.6929-2.7270.32841520.21982883X-RAY DIFFRACTION98
2.727-2.76290.32061510.21752868X-RAY DIFFRACTION98
2.7629-2.80070.26871530.20392916X-RAY DIFFRACTION98
2.8007-2.84070.32821540.2092911X-RAY DIFFRACTION98
2.8407-2.88310.2871510.20322876X-RAY DIFFRACTION98
2.8831-2.92820.2491510.22876X-RAY DIFFRACTION98
2.9282-2.97620.29811540.2012910X-RAY DIFFRACTION98
2.9762-3.02750.27291510.20172886X-RAY DIFFRACTION98
3.0275-3.08250.28891540.19432908X-RAY DIFFRACTION98
3.0825-3.14180.25141520.18882897X-RAY DIFFRACTION98
3.1418-3.20590.26591550.18932947X-RAY DIFFRACTION98
3.2059-3.27560.27361520.1942887X-RAY DIFFRACTION98
3.2756-3.35180.24711530.17942902X-RAY DIFFRACTION98
3.3518-3.43560.2311510.16932876X-RAY DIFFRACTION97
3.4356-3.52850.18571540.16982915X-RAY DIFFRACTION98
3.5285-3.63230.24931520.16052890X-RAY DIFFRACTION98
3.6323-3.74950.21481530.15942910X-RAY DIFFRACTION97
3.7495-3.88340.19521510.15862873X-RAY DIFFRACTION97
3.8834-4.03880.22341520.15592889X-RAY DIFFRACTION97
4.0388-4.22260.20711540.14462917X-RAY DIFFRACTION98
4.2226-4.44510.17771540.14042940X-RAY DIFFRACTION98
4.4451-4.72330.18071560.13982948X-RAY DIFFRACTION98
4.7233-5.08770.1781540.14552939X-RAY DIFFRACTION98
5.0877-5.5990.19481560.1592951X-RAY DIFFRACTION98
5.599-6.40770.22921540.17282938X-RAY DIFFRACTION97
6.4077-8.06730.20981560.16772957X-RAY DIFFRACTION96
8.0673-49.2060.18931660.17833144X-RAY DIFFRACTION98

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