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

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Basic information

Entry
Database: PDB / ID: 4xpr
TitleCrystal structure of the mutant D365A of Pedobacter saltans GH31 alpha-galactosidase
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
Biological speciesPedobacter saltans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7567
Polymers81,3841
Non-polymers3726
Water9,422523
1
A: Alpha-glucosidase
hetero molecules

A: Alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,51314
Polymers162,7682
Non-polymers74512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area7590 Å2
ΔGint24 kcal/mol
Surface area45340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.028, 112.028, 114.752
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-1507-

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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 20% PEG MME 2000, 100 mM HEPES-NaOH

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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: Nov 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 49262 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 20.1
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 3.4 / % possible all: 99.9

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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: 2.01→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.428 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18487 2457 5.1 %RANDOM
Rwork0.15026 ---
obs0.15201 46080 98.29 %-
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: 27.598 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.01→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5335 0 24 523 5882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.025521
X-RAY DIFFRACTIONr_bond_other_d0.0010.025123
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.9577469
X-RAY DIFFRACTIONr_angle_other_deg0.767311831
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4735665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3523.619257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46615904
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4771531
X-RAY DIFFRACTIONr_chiral_restr0.0820.2749
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216238
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021311
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_it1.4892.552660
X-RAY DIFFRACTIONr_mcbond_other1.4882.5492659
X-RAY DIFFRACTIONr_mcangle_it2.1933.8143322
X-RAY DIFFRACTIONr_mcangle_other2.1933.8153323
X-RAY DIFFRACTIONr_scbond_it2.1522.7842861
X-RAY DIFFRACTIONr_scbond_other2.1522.7842861
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3874.0554147
X-RAY DIFFRACTIONr_long_range_B_refined4.98621.4766778
X-RAY DIFFRACTIONr_long_range_B_other4.78621.0936565
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.007→2.059 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 160 -
Rwork0.192 2880 -
obs--84.42 %

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