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

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Basic information

Entry
Database: PDB / ID: 4fnp
TitleCrystal structure of GH36 alpha-galactosidase AgaA A355E from Geobacillus stearothermophilus
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
Alpha-galactosidase AgaA
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 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 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)334,35216
Polymers333,1994
Non-polymers1,15312
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22960 Å2
ΔGint-54 kcal/mol
Surface area85160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.500, 150.500, 234.100
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 20% PEG 3350, 0.2M sodium iodide, 10% ethylene glycol, 5% polyvinyl pyrrolidone K15, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 1, 2005
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 76055 / Num. obs: 75205 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 15.1 Å2 / Rsym value: 0.122 / Net I/σ(I): 11.28
Reflection shellResolution: 2.8→3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 3.85 / % possible all: 96.2

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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 / Resolution: 2.803→19.833 Å / SU ML: 0.3 / σ(F): 2 / Phase error: 22.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2471 3761 5 %
Rwork0.1944 --
obs0.197 75201 99.58 %
all-75201 -
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--9.7807 Å2-0 Å2-0 Å2
2---9.7807 Å2-0 Å2
3----9.5577 Å2
Refinement stepCycle: LAST / Resolution: 2.803→19.833 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23148 0 60 71 23279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223780
X-RAY DIFFRACTIONf_angle_d0.65632252
X-RAY DIFFRACTIONf_dihedral_angle_d12.3578760
X-RAY DIFFRACTIONf_chiral_restr0.0493376
X-RAY DIFFRACTIONf_plane_restr0.0024220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8034-2.83880.31961250.26242374X-RAY DIFFRACTION91
2.8388-2.8760.3191370.24892594X-RAY DIFFRACTION100
2.876-2.91530.32031390.24052645X-RAY DIFFRACTION100
2.9153-2.95680.31951390.23452646X-RAY DIFFRACTION100
2.9568-3.00080.26021390.23492643X-RAY DIFFRACTION100
3.0008-3.04750.29121370.23512590X-RAY DIFFRACTION100
3.0475-3.09730.3221390.23162637X-RAY DIFFRACTION100
3.0973-3.15050.29361380.23162635X-RAY DIFFRACTION100
3.1505-3.20760.30861390.22832643X-RAY DIFFRACTION100
3.2076-3.2690.29531400.22342648X-RAY DIFFRACTION100
3.269-3.33540.28051360.21452599X-RAY DIFFRACTION100
3.3354-3.40760.28351390.212623X-RAY DIFFRACTION100
3.4076-3.48650.25331390.20772652X-RAY DIFFRACTION100
3.4865-3.57320.2491420.19882687X-RAY DIFFRACTION100
3.5732-3.66920.26211370.19482614X-RAY DIFFRACTION99
3.6692-3.77640.23251380.18572618X-RAY DIFFRACTION100
3.7764-3.89740.23591390.17612636X-RAY DIFFRACTION100
3.8974-4.03560.22431390.17752642X-RAY DIFFRACTION100
4.0356-4.19570.21491400.16042671X-RAY DIFFRACTION100
4.1957-4.38470.22331400.15392658X-RAY DIFFRACTION100
4.3847-4.61320.20071400.15042665X-RAY DIFFRACTION100
4.6132-4.89810.18491410.15152665X-RAY DIFFRACTION100
4.8981-5.26970.20681410.17052680X-RAY DIFFRACTION100
5.2697-5.7880.22651420.17812709X-RAY DIFFRACTION100
5.788-6.59840.24291420.19322697X-RAY DIFFRACTION100
6.5984-8.21390.19511450.18332743X-RAY DIFFRACTION100
8.2139-19.83310.16761490.17292826X-RAY DIFFRACTION100

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