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- PDB-4fnu: Crystal structure of GH36 alpha-galactosidase AgaA A355E D478A fr... -

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Basic information

Entry
Database: PDB / ID: 4fnu
TitleCrystal structure of GH36 alpha-galactosidase AgaA A355E D478A from Geobacillus stearothermophilus in complex with stachyose
ComponentsAlpha-galactosidase AgaA
KeywordsHYDROLASE / Glycoside Hydrolase / carbohydrate
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 / Glycoside hydrolase superfamily / Aldolase-type TIM barrel / 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: 3.6 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 / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)335,9548
Polymers333,2884
Non-polymers2,6664
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30040 Å2
ΔGint10 kcal/mol
Surface area85650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.070, 154.070, 238.020
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: 83321.930 Da / Num. of mol.: 4 / Mutation: A355E, D478A
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
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose-(1-6)-alpha-D-galactopyranose-(1-6)-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DFrufb2-1DGlcpa1-6DGalpa1-6DGalpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[ha122h-2b_2-5][a2122h-1a_1-5][a2112h-1a_1-5]/1-2-3-3/a2-b1_b6-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{[(6+1)][a-D-Galp]{[(6+1)][a-D-Galp]{}}}}LINUCSPDB-CARE
Nonpolymer detailsTHE COMPOUND Β-D-FRUCTOFURANOSYL-O-Α-D -GALACTOPYRANOSYL-(1→6)-O-Α-D - ...THE COMPOUND Β-D-FRUCTOFURANOSYL-O-Α-D -GALACTOPYRANOSYL-(1→6)-O-Α-D -GALACTOPYRANOSYL-(1→6)-Α- D-GLUCOPYRANOSIDE, REPRESENTS THE CHEMICAL ENTITY STACHYOSE

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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: 2.45 Å3/Da / Density % sol: 49.73 %
Crystal growTemperature: 292 K / pH: 8.5
Details: 12% polyethylene glycol 4000, 0.1M Tris, 0.02M stachyose, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2012
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→20 Å / Num. obs: 38121 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 75.5 Å2 / Rsym value: 0.094 / Net I/σ(I): 18.48
Reflection shellResolution: 3.6→3.69 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→19.922 Å / SU ML: 0.52 / σ(F): 1.99 / Phase error: 29.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2822 1904 5 %
Rwork0.2377 --
obs0.24 38114 99.67 %
all-38114 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→19.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23152 0 180 0 23332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323932
X-RAY DIFFRACTIONf_angle_d0.73232472
X-RAY DIFFRACTIONf_dihedral_angle_d19.549104
X-RAY DIFFRACTIONf_chiral_restr0.0463372
X-RAY DIFFRACTIONf_plane_restr0.0034220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6001-3.68960.38661340.34672560X-RAY DIFFRACTION100
3.6896-3.78870.38651340.3152538X-RAY DIFFRACTION100
3.7887-3.89940.35331340.30562557X-RAY DIFFRACTION100
3.8994-4.02420.40921350.3122560X-RAY DIFFRACTION100
4.0242-4.16680.32161360.28172576X-RAY DIFFRACTION100
4.1668-4.3320.30491340.26582553X-RAY DIFFRACTION100
4.332-4.5270.33531360.24882577X-RAY DIFFRACTION100
4.527-4.76260.2851350.23962563X-RAY DIFFRACTION100
4.7626-5.05640.27171350.22852574X-RAY DIFFRACTION100
5.0564-5.43940.30411370.2252601X-RAY DIFFRACTION100
5.4394-5.97340.26111370.22892602X-RAY DIFFRACTION100
5.9734-6.80740.2581360.22142592X-RAY DIFFRACTION99
6.8074-8.46560.2411400.20262646X-RAY DIFFRACTION100
8.4656-19.92250.17771410.16632711X-RAY DIFFRACTION99

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