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- PDB-4fnq: Crystal structure of GH36 alpha-galactosidase AgaB from Geobacill... -

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Basic information

Entry
Database: PDB / ID: 4fnq
TitleCrystal structure of GH36 alpha-galactosidase AgaB from Geobacillus stearothermophilus
ComponentsAlpha-galactosidase AgaB
KeywordsHYDROLASE / Glycoside Hydrolase
Function / homology
Function and homology information


raffinose alpha-galactosidase activity / alpha-galactosidase / carbohydrate catabolic process
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
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Alpha-galactosidase AgaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6292
Polymers83,5671
Non-polymers621
Water7,134396
1
A: Alpha-galactosidase AgaB
hetero molecules

A: Alpha-galactosidase AgaB
hetero molecules

A: Alpha-galactosidase AgaB
hetero molecules

A: Alpha-galactosidase AgaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,5178
Polymers334,2694
Non-polymers2484
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area23060 Å2
ΔGint-46 kcal/mol
Surface area85770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.300, 113.100, 161.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1089-

HOH

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Components

#1: Protein Alpha-galactosidase AgaB


Mass: 83567.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: agaB / Production host: Escherichia coli (E. coli) / References: UniProt: Q934H7, alpha-galactosidase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.7M ammonium sulfate 20mM HEPES, pH 6.5, VAPOR DIFFUSION, HANGING 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: 1.7→20 Å / Num. all: 87928 / Num. obs: 84878 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 22.1 Å2 / Rsym value: 0.045 / Net I/σ(I): 27.39
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 2 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 5.1 / % possible all: 73.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.471 Å / SU ML: 0.15 / σ(F): 1.99 / Phase error: 20.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2089 3659 5 %
Rwork0.1811 --
obs0.1825 73179 98.75 %
all-84833 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1456 Å20 Å2-0 Å2
2--0.0118 Å2-0 Å2
3----0.1574 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.471 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5832 0 4 396 6232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075985
X-RAY DIFFRACTIONf_angle_d1.1728111
X-RAY DIFFRACTIONf_dihedral_angle_d14.2392210
X-RAY DIFFRACTIONf_chiral_restr0.083846
X-RAY DIFFRACTIONf_plane_restr0.0051063
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82370.28021360.22022606X-RAY DIFFRACTION98
1.8237-1.84860.21541380.2222615X-RAY DIFFRACTION98
1.8486-1.8750.26411360.22632584X-RAY DIFFRACTION96
1.875-1.9030.28451360.22672583X-RAY DIFFRACTION96
1.903-1.93270.22931380.21372624X-RAY DIFFRACTION98
1.9327-1.96440.2211390.20522640X-RAY DIFFRACTION99
1.9644-1.99820.21781430.18422704X-RAY DIFFRACTION100
1.9982-2.03450.20971400.17192671X-RAY DIFFRACTION100
2.0345-2.07360.21811430.16762706X-RAY DIFFRACTION100
2.0736-2.11590.2021390.16722648X-RAY DIFFRACTION100
2.1159-2.16180.22211410.1792686X-RAY DIFFRACTION100
2.1618-2.2120.21191400.18132656X-RAY DIFFRACTION99
2.212-2.26730.18291410.1742681X-RAY DIFFRACTION99
2.2673-2.32850.2041400.17642651X-RAY DIFFRACTION99
2.3285-2.39690.23141410.17352690X-RAY DIFFRACTION99
2.3969-2.47410.19751400.18062663X-RAY DIFFRACTION99
2.4741-2.56230.19681430.17852710X-RAY DIFFRACTION99
2.5623-2.66470.21421400.18122656X-RAY DIFFRACTION99
2.6647-2.78560.19571420.17842693X-RAY DIFFRACTION99
2.7856-2.9320.22241420.18542706X-RAY DIFFRACTION99
2.932-3.1150.20031420.18092695X-RAY DIFFRACTION99
3.115-3.35440.2061440.17412731X-RAY DIFFRACTION100
3.3544-3.68990.20151430.16682714X-RAY DIFFRACTION100
3.6899-4.21910.16951430.16152730X-RAY DIFFRACTION99
4.2191-5.29790.18081440.16532732X-RAY DIFFRACTION98
5.2979-19.47240.25751450.21112745X-RAY DIFFRACTION95

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