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- PDB-4xps: Crystal structure of the mutant D365A of Pedobacter saltans GH31 ... -

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Basic information

Entry
Database: PDB / ID: 4xps
TitleCrystal structure of the mutant D365A of Pedobacter saltans GH31 alpha-galactosidase complexed with p-nitrophenyl-alpha-galactopyranoside
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
alpha-D-galactopyranose / P-NITROPHENOL / Alpha-galactosidase
Similarity search - Component
Biological speciesPedobacter saltans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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)81,8896
Polymers81,3841
Non-polymers5055
Water5,819323
1
A: Alpha-glucosidase
hetero molecules

A: Alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,77912
Polymers162,7682
Non-polymers1,01110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area7860 Å2
ΔGint24 kcal/mol
Surface area45340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.954, 111.954, 113.991
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1372-

HOH

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Components

#1: Protein Alpha-glucosidase


Mass: 81383.844 Da / Num. of mol.: 1 / Mutation: D365A
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-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 323 / 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. AND RESIDUE 365 ALA REPRESENTS MUTATION (D365A).

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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: 2.19 Å3/Da / Density % sol: 43.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG MME 2000, 100 mM HEPES-NaOH, soaked with 20 mM pNP-alpha-galactopyranoside

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 42959 / % possible obs: 99.3 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 24.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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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: 2.1→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.799 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24906 2066 5 %RANDOM
Rwork0.19707 ---
obs0.19963 39532 97.05 %-
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: 32.018 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5332 0 33 323 5688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.025524
X-RAY DIFFRACTIONr_bond_other_d0.0010.025113
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.9597476
X-RAY DIFFRACTIONr_angle_other_deg0.781311807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6225663
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34623.569255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18515901
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6071531
X-RAY DIFFRACTIONr_chiral_restr0.0820.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216235
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021314
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_it1.7453.0452658
X-RAY DIFFRACTIONr_mcbond_other1.7433.0442657
X-RAY DIFFRACTIONr_mcangle_it2.5584.5573319
X-RAY DIFFRACTIONr_mcangle_other2.5584.5583320
X-RAY DIFFRACTIONr_scbond_it2.1563.2712866
X-RAY DIFFRACTIONr_scbond_other2.1563.2712866
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3064.7964158
X-RAY DIFFRACTIONr_long_range_B_refined4.97828.9924662
X-RAY DIFFRACTIONr_long_range_B_other4.94728.96224498
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 129 -
Rwork0.244 2782 -
obs--93.69 %

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