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- PDB-8j52: Crystal structure of Flavihumibacter petaseus GH31 alpha-galactos... -

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Basic information

Entry
Database: PDB / ID: 8j52
TitleCrystal structure of Flavihumibacter petaseus GH31 alpha-galactosidase mutant D304A in complex with alpha-1,4-galactobiose
ComponentsGH31 alpha-galactosidase
KeywordsHYDROLASE / Glycoside hydrolase / (beta/alpha)8 barrel / Globo sphingolipid / glycolipid / Carbohydrate
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
: / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
beta-D-galactopyranose / alpha-D-galactopyranose / Putative glycosidase
Similarity search - Component
Biological speciesFlavihumibacter petaseus NBRC 106054 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsIkegaya, M. / Miyazaki, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K15748 Japan
CitationJournal: Febs J. / Year: 2023
Title: Structure-function analysis of bacterial GH31 alpha-galactosidases specific for alpha-(1→4)-galactobiose.
Authors: Ikegaya, M. / Park, E.Y. / Miyazaki, T.
History
DepositionApr 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GH31 alpha-galactosidase
B: GH31 alpha-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,33319
Polymers121,8592
Non-polymers1,47417
Water14,304794
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint36 kcal/mol
Surface area35810 Å2
Unit cell
Length a, b, c (Å)71.499, 72.543, 81.202
Angle α, β, γ (deg.)101.922, 104.396, 103.708
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein GH31 alpha-galactosidase


Mass: 60929.332 Da / Num. of mol.: 2 / Mutation: D304A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavihumibacter petaseus NBRC 106054 (bacteria)
Strain: NBRC 106054 / Gene: FPE01S_01_01430 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0E9MUN5, alpha-galactosidase

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Sugars , 2 types, 4 molecules

#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.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
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: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
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

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Non-polymers , 3 types, 807 molecules

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


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 794 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.12 Å3/Da / Density % sol: 60.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 1 M sodium chloride, 50 mM MES-NaOH, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→46.044 Å / Num. obs: 113161 / % possible obs: 97.4 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.071 / Rrim(I) all: 0.101 / Net I/σ(I): 7.8
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5559 / CC1/2: 0.769 / Rpim(I) all: 0.494 / Rrim(I) all: 0.699

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46.044 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.177 / WRfactor Rwork: 0.125 / SU B: 7.089 / SU ML: 0.088 / Average fsc free: 0.9773 / Average fsc work: 0.9902 / Cross valid method: FREE R-VALUE / ESU R: 0.154 / ESU R Free: 0.108
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1922 5585 4.935 %
Rwork0.1361 107575 -
all0.139 --
obs-113160 97.443 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 23.858 Å2
Baniso -1Baniso -2Baniso -3
1-1.449 Å2-0.253 Å2-1.694 Å2
2--0.213 Å20.206 Å2
3----0.423 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8091 0 92 794 8977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0128412
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167881
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.64311385
X-RAY DIFFRACTIONr_angle_other_deg0.5661.56718111
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78651020
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.247561
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.546101369
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.14210395
X-RAY DIFFRACTIONr_chiral_restr0.0840.21192
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029886
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022074
X-RAY DIFFRACTIONr_nbd_refined0.2210.21570
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.27242
X-RAY DIFFRACTIONr_nbtor_refined0.1860.24034
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.24286
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2530
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0470.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3410.24
X-RAY DIFFRACTIONr_nbd_other0.220.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1760.219
X-RAY DIFFRACTIONr_mcbond_it1.9492.3654074
X-RAY DIFFRACTIONr_mcbond_other1.9482.3654074
X-RAY DIFFRACTIONr_mcangle_it2.6394.2485087
X-RAY DIFFRACTIONr_mcangle_other2.6424.2495088
X-RAY DIFFRACTIONr_scbond_it2.3782.6884338
X-RAY DIFFRACTIONr_scbond_other2.3782.6894339
X-RAY DIFFRACTIONr_scangle_it3.2484.7876295
X-RAY DIFFRACTIONr_scangle_other3.2484.7876296
X-RAY DIFFRACTIONr_lrange_it3.66923.699616
X-RAY DIFFRACTIONr_lrange_other3.58122.9729489
X-RAY DIFFRACTIONr_rigid_bond_restr5.543316293
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.9-1.9490.2644000.20778790.20986090.9610.98296.16680.198
1.949-2.0030.2444380.18676130.1983550.9730.98596.36150.174
2.003-2.0610.2263830.16874590.17181290.9730.98896.46940.151
2.061-2.1240.213810.15672590.15879030.9770.9996.67210.138
2.124-2.1930.2123660.15270490.15576590.9740.9996.81420.13
2.193-2.270.2153680.14168370.14574240.9760.99197.05010.121
2.27-2.3560.2023930.13665310.1471220.9770.99197.21990.114
2.356-2.4520.1843230.1263490.12468620.9820.99397.23110.1
2.452-2.560.1962950.12661460.12966030.9810.99397.54660.105
2.56-2.6850.2143090.12558800.12963240.9740.99397.86530.104
2.685-2.8290.1662720.12355750.12559750.9840.99397.85770.104
2.829-30.1962580.12353240.12756990.9760.99297.9470.107
3-3.2070.2042650.12949460.13353000.9750.99198.32080.116
3.207-3.4620.182780.13346220.13549790.9820.99198.41330.125
3.462-3.790.191940.13743050.1445630.9840.99198.59740.133
3.79-4.2340.1471860.11538940.11641380.9870.99398.59840.113
4.234-4.8820.1531830.10634240.10836440.9890.99598.98460.107
4.882-5.9630.1921140.13229400.13430910.9860.99398.8030.13
5.963-8.3630.1721110.13322540.13423810.9840.99199.3280.131
8.363-46.0440.173680.18612900.18513650.9890.98399.48720.212

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