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- PDB-8iuc: Crystal structure of GH65 alpha-1,2-glucosidase from Flavobacteri... -

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Basic information

Entry
Database: PDB / ID: 8iuc
TitleCrystal structure of GH65 alpha-1,2-glucosidase from Flavobacterium johnsoniae in complex with isomaltose
ComponentsCandidate alpha glycoside phosphorylase Glycoside hydrolase family 65
KeywordsHYDROLASE / glycoside hydrolase / GH65 / kojibiose / (alpha/alpha)6-barrel / dextran
Function / homology
Function and homology information


kojibiose hydrolase / glycosyltransferase activity / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process / periplasmic space
Similarity search - Function
Glycoside hydrolase, family 65, central catalytic / Glycoside hydrolase, family 65, N-terminal / Glycosyl hydrolase family 65 central catalytic domain / Glycosyl hydrolase family 65, N-terminal domain / Glycoside hydrolase family 65, N-terminal domain superfamily / Galactose mutarotase-like domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
Biological speciesFlavobacterium johnsoniae UW101 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsNakamura, S. / Miyazaki, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K15748 Japan
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Bacteroidota polysaccharide utilization system for branched dextran exopolysaccharides from lactic acid bacteria.
Authors: Nakamura, S. / Kurata, R. / Tonozuka, T. / Funane, K. / Park, E.Y. / Miyazaki, T.
History
DepositionMar 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65
B: Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65
C: Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,35736
Polymers229,4683
Non-polymers2,88933
Water25,4731414
1
A: Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65
B: Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65
C: Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65
hetero molecules

A: Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65
B: Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65
C: Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65
hetero molecules


Theoretical massNumber of molelcules
Total (without water)464,71372
Polymers458,9356
Non-polymers5,77866
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)122.938, 194.090, 111.880
Angle α, β, γ (deg.)90.000, 116.348, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-1255-

HOH

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Components

#1: Protein Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65 / alpha-1 / 2-glucosidase


Mass: 76489.219 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae UW101 (bacteria)
Gene: Fjoh_4428 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5FBJ5
#2: Polysaccharide alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(6+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1414 / Source method: isolated from a natural source / Formula: H2O
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: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 300mM ammonium citrate, pH 7.0-8.0, 10mM TCEP, 12% PEG 3350
PH range: 7.0-8.0

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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 PILATUS 2M / Detector: PIXEL / Date: Jun 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→48.54 Å / Num. obs: 326516 / % possible obs: 98.2 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.049 / Rrim(I) all: 0.088 / Net I/σ(I): 13.2
Reflection shellResolution: 1.56→1.59 Å / Rmerge(I) obs: 0.947 / Mean I/σ(I) obs: 2 / Num. unique obs: 326516 / CC1/2: 0.813 / Rpim(I) all: 0.644 / Rrim(I) all: 1.15

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→44.71 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.073 / SU ML: 0.084 / Cross valid method: FREE R-VALUE / ESU R: 0.081 / ESU R Free: 0.08
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2114 16344 5.01 %
Rwork0.1873 309888 -
all0.188 --
obs-326232 98.263 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.71 Å2
Baniso -1Baniso -2Baniso -3
1--2.046 Å20 Å21.149 Å2
2---3.159 Å2-0 Å2
3---2.728 Å2
Refinement stepCycle: LAST / Resolution: 1.56→44.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15741 0 189 1414 17344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01216579
X-RAY DIFFRACTIONr_bond_other_d0.0010.01615453
X-RAY DIFFRACTIONr_angle_refined_deg1.9741.65222505
X-RAY DIFFRACTIONr_angle_other_deg0.6731.57235699
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.06352054
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.312562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.994102815
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.99110770
X-RAY DIFFRACTIONr_chiral_restr0.1070.22446
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0219269
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023797
X-RAY DIFFRACTIONr_nbd_refined0.2290.23242
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.214415
X-RAY DIFFRACTIONr_nbtor_refined0.1880.27919
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.28560
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.21247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0010.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1730.220
X-RAY DIFFRACTIONr_nbd_other0.1550.2161
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1610.291
X-RAY DIFFRACTIONr_mcbond_it1.4541.3728054
X-RAY DIFFRACTIONr_mcbond_other1.4541.3728054
X-RAY DIFFRACTIONr_mcangle_it1.9412.46210111
X-RAY DIFFRACTIONr_mcangle_other1.9422.46210112
X-RAY DIFFRACTIONr_scbond_it2.5011.6328525
X-RAY DIFFRACTIONr_scbond_other2.51.6328526
X-RAY DIFFRACTIONr_scangle_it3.6482.8612377
X-RAY DIFFRACTIONr_scangle_other3.6482.8612378
X-RAY DIFFRACTIONr_lrange_it5.34214.86419166
X-RAY DIFFRACTIONr_lrange_other5.31513.60518840
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
1.56-1.60.33511940.318226350.319245570.8620.87397.03550.291
1.6-1.6440.31611660.301220410.302238810.8710.88997.17770.273
1.644-1.6920.28711080.282215160.283232090.9130.90797.47940.253
1.692-1.7440.26210960.252208920.253225220.930.93597.6290.225
1.744-1.8010.24911000.231203250.232219060.940.94997.80430.203
1.801-1.8640.23410520.21196580.212211400.9510.96197.96590.184
1.864-1.9340.2289930.193189990.194203720.9590.97198.13470.17
1.934-2.0130.21610340.181182490.183196580.9670.97798.09240.161
2.013-2.1020.2179260.18176190.182188530.9690.97898.36630.16
2.102-2.2050.2118770.173168580.175180250.970.9898.39110.155
2.205-2.3240.2198200.172160600.174171240.9670.98198.57510.155
2.324-2.4640.2017550.162152780.163162370.9750.98498.74360.147
2.464-2.6340.2187140.162143650.164152400.9710.98498.94360.149
2.634-2.8440.1897170.164133830.165142100.9760.98499.22590.155
2.844-3.1140.1996450.173123680.174131080.9750.98299.27520.167
3.114-3.480.25760.186111820.187118290.9770.98299.39980.185
3.48-4.0140.1815520.16998570.17104450.9830.98599.65530.173
4.014-4.9060.1594330.14884050.14988570.9860.98899.78550.16
4.906-6.8970.2113830.19664980.19768980.9830.98799.75360.207
6.897-44.710.182030.16937020.1739150.9830.98699.74460.185
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4817-0.1567-0.28681.20390.59650.5867-0.00620.0975-0.0709-0.0931-0.08160.2833-0.0189-0.1630.08770.0954-0.0081-0.00350.09440.00360.0993-35.036-11.9910.112
21.02990.16740.24681.10150.04880.63690.0029-0.18710.13150.1929-0.0480.2616-0.0076-0.05880.04520.13050.01820.06890.0902-0.02390.0777-30.81711.87824.953
30.4223-0.0550.07531.7112-0.17920.9521-0.0058-0.04730.18820.0058-0.0965-0.3403-0.13830.19820.10230.1166-0.006-0.00530.12280.00950.144217.2338.87220.311
40.42490.1391-0.00261.1734-0.37280.75190.035-0.1840.0640.322-0.0938-0.0963-0.01280.07970.05880.1686-0.0174-0.01550.1479-0.02280.023610.902-0.66234.557
51.0955-0.0688-0.06780.7841-0.20150.30890.0067-0.0319-0.17010.0695-0.023-0.10770.07190.0430.01640.13880.0140.00090.07440.00550.051611.031-41.76416.968
61.0804-0.15420.20410.9492-0.09790.5209-0.0041-0.2069-0.12940.18910.01580.13020.0103-0.072-0.01170.1552-0.03040.05330.0980.01770.0373-24.167-42.81526.705
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA23 - 353
2X-RAY DIFFRACTION2ALLA354 - 681

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