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- PDB-8iua: Crystal structure of GH66 endodextranase from Flavobacterium john... -

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Basic information

Entry
Database: PDB / ID: 8iua
TitleCrystal structure of GH66 endodextranase from Flavobacterium johnsoniae in complex with isomaltose
ComponentsCandidate dextranase Glycoside hydrolase family 66
KeywordsHYDROLASE / glycoside hydrolase / GH66 / dextran / TIM-barrel
Function / homology
Function and homology information


Glycosyl hydrolase family 66 / Glycosyl hydrolase family 66 / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / Candidate dextranase Glycoside hydrolase family 66
Similarity search - Component
Biological speciesFlavobacterium johnsoniae UW101 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 dextranase Glycoside hydrolase family 66
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1244
Polymers64,5791
Non-polymers5453
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: PISA analysis predicted it as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-6 kcal/mol
Surface area20750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.712, 47.996, 76.477
Angle α, β, γ (deg.)90.000, 104.640, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-963-

HOH

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Components

#1: Protein Candidate dextranase Glycoside hydrolase family 66


Mass: 64578.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae UW101 (bacteria)
Gene: Fjoh_4431 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5FBI2
#2: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


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


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100mM Tris-HCl, pH 8.5-9.0, 200mM lithium sulfate, 20% PEG 4000
PH range: 8.5-9.0

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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: Mar 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→46.9 Å / Num. obs: 50250 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.077 / Rrim(I) all: 0.144 / Net I/σ(I): 11
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 50250 / CC1/2: 0.839 / Rpim(I) all: 0.57 / Rrim(I) all: 1.085

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→46.9 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU B: 10.231 / SU ML: 0.153 / Cross valid method: FREE R-VALUE / ESU R: 0.154 / ESU R Free: 0.145
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2527 2536 5.047 %
Rwork0.2083 47713 -
all0.21 --
obs-50249 99.679 %
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: 28.622 Å2
Baniso -1Baniso -2Baniso -3
1--1.337 Å20 Å20.696 Å2
2--0.752 Å20 Å2
3---0.195 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4398 0 36 268 4702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124545
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164120
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.6446180
X-RAY DIFFRACTIONr_angle_other_deg0.511.5749485
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.85554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.314510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47710724
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.05110225
X-RAY DIFFRACTIONr_chiral_restr0.0730.2667
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025322
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021086
X-RAY DIFFRACTIONr_nbd_refined0.2250.2892
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.24019
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22257
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22378
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2305
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0120.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0860.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0650.211
X-RAY DIFFRACTIONr_nbd_other0.190.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.110.217
X-RAY DIFFRACTIONr_mcbond_it0.7070.4042219
X-RAY DIFFRACTIONr_mcbond_other0.7070.4042219
X-RAY DIFFRACTIONr_mcangle_it0.9750.722772
X-RAY DIFFRACTIONr_mcangle_other0.9750.722773
X-RAY DIFFRACTIONr_scbond_it0.9150.5182326
X-RAY DIFFRACTIONr_scbond_other0.9170.522327
X-RAY DIFFRACTIONr_scangle_it1.3690.9083408
X-RAY DIFFRACTIONr_scangle_other1.3690.913409
X-RAY DIFFRACTIONr_lrange_it5.6085.055286
X-RAY DIFFRACTIONr_lrange_other5.624.5745251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.3331740.3013514X-RAY DIFFRACTION98.7945
1.847-1.8970.3181680.2973390X-RAY DIFFRACTION99.9158
1.897-1.9520.31800.2763290X-RAY DIFFRACTION99.0862
1.952-2.0120.2951760.2533234X-RAY DIFFRACTION99.2722
2.012-2.0780.2681850.2413091X-RAY DIFFRACTION99.8781
2.078-2.1510.2711590.2333032X-RAY DIFFRACTION99.6254
2.151-2.2320.2871590.2192922X-RAY DIFFRACTION99.612
2.232-2.3230.2631520.2112796X-RAY DIFFRACTION99.7631
2.323-2.4260.2631410.2122704X-RAY DIFFRACTION99.7546
2.426-2.5440.2711450.2192589X-RAY DIFFRACTION99.8904
2.544-2.6810.2751420.2182466X-RAY DIFFRACTION99.9234
2.681-2.8430.2721280.2052332X-RAY DIFFRACTION100
2.843-3.0380.2841220.2092191X-RAY DIFFRACTION100
3.038-3.2810.2391090.1962046X-RAY DIFFRACTION99.8147
3.281-3.5920.2171020.1881892X-RAY DIFFRACTION100
3.592-4.0130.219830.1731750X-RAY DIFFRACTION100
4.013-4.6280.165710.1511515X-RAY DIFFRACTION99.937
4.628-5.6550.214570.1631322X-RAY DIFFRACTION99.8552
5.655-7.940.215470.1811033X-RAY DIFFRACTION100
7.94-46.90.178360.172604X-RAY DIFFRACTION100
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)
11.53130.5340.65451.08180.14460.73930.0092-0.0529-0.06380.0951-0.0263-0.06970.05940.00220.01710.71690.02510.00970.01220.00140.0104-21.21-32.022-19.191
21.01320.0742-0.39330.7236-0.01060.8165-0.01880.03440.06130.0978-0.02430.0666-0.0228-0.06540.04310.71650.0082-0.00750.0063-0.00550.0157-29.876-18.175-17.274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA32 - 259
2X-RAY DIFFRACTION2ALLA260 - 586

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