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- PDB-4xpp: Crystal structure of Pedobacter saltans GH31 alpha-galactosidase ... -

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Basic information

Entry
Database: PDB / ID: 4xpp
TitleCrystal structure of Pedobacter saltans GH31 alpha-galactosidase complexed with D-galactose
ComponentsAlpha-glucosidase
KeywordsHYDROLASE / TIM-barrel / GH31
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Domain of unknown function DUF5110 / Domain of unknown function (DUF5110) / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Glycosyl hydrolase, all-beta ...Domain of unknown function DUF5110 / Domain of unknown function (DUF5110) / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-D-galactopyranose / Alpha-galactosidase
Similarity search - Component
Biological speciesPedobacter saltans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMiyazaki, T. / Ishizaki, Y. / Ichikawa, M. / Nishikawa, A. / Tonozuka, T.
CitationJournal: Biochem.J. / Year: 2015
Title: Structural and biochemical characterization of novel bacterial alpha-galactosidases belonging to glycoside hydrolase family 31
Authors: Miyazaki, T. / Ishizaki, Y. / Ichikawa, M. / Nishikawa, A. / Tonozuka, T.
History
DepositionJan 17, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / citation ...chem_comp / citation / diffrn_source / pdbx_struct_oper_list
Item: _chem_comp.type / _citation.journal_id_CSD ..._chem_comp.type / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7324
Polymers81,4281
Non-polymers3043
Water4,432246
1
A: Alpha-glucosidase
hetero molecules

A: Alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,4648
Polymers162,8562
Non-polymers6096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6650 Å2
ΔGint6 kcal/mol
Surface area45910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.792, 111.792, 115.414
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Alpha-glucosidase


Mass: 81427.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pedobacter saltans (bacteria) / Strain: NBRC 100064 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0F7R6D6*PLUS, alpha-galactosidase
#2: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS BASED ON GENBANK BAR72452.1. N-TERMINAL RESIDUES MGSSHHHHHHSSGLVPRGSHMA REPRESENT ...THE SEQUENCE IS BASED ON GENBANK BAR72452.1. N-TERMINAL RESIDUES MGSSHHHHHHSSGLVPRGSHMA REPRESENT EXPRESSION TAGS.

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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: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG MME 2000, 100 mM HEPES-NaOH, 50 mM galactose
PH range: 7.5 - 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 32895 / % possible obs: 99.9 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 32.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 5.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data processing
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XPO

4xpo


Resolution: 2.3→39.52 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19192 1667 5.1 %RANDOM
Rwork0.15222 ---
obs0.15421 31149 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.662 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0 Å2
2--0.04 Å20 Å2
3----0.08 Å2
Refinement stepCycle: 1 / Resolution: 2.3→39.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5335 0 20 246 5601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.025514
X-RAY DIFFRACTIONr_bond_other_d00.025102
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9587467
X-RAY DIFFRACTIONr_angle_other_deg3.58311782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5255663
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81823.594256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41615902
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6631531
X-RAY DIFFRACTIONr_chiral_restr0.0820.2753
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216227
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021310
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2833.9482658
X-RAY DIFFRACTIONr_mcbond_other2.2763.9472657
X-RAY DIFFRACTIONr_mcangle_it3.3445.9113319
X-RAY DIFFRACTIONr_mcangle_other3.3445.9123320
X-RAY DIFFRACTIONr_scbond_it2.964.2622856
X-RAY DIFFRACTIONr_scbond_other2.964.2622856
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6456.2324149
X-RAY DIFFRACTIONr_long_range_B_refined5.76631.9416434
X-RAY DIFFRACTIONr_long_range_B_other5.76331.8576366
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.304→2.364 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 125 -
Rwork0.183 2188 -
obs--96.42 %

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