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- PDB-8iu9: Crystal structure of GH66 endodextranase from Flavobacterium john... -

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Basic information

Entry
Database: PDB / ID: 8iu9
TitleCrystal structure of GH66 endodextranase from Flavobacterium johnsoniae in complex with glucose
ComponentsCandidate dextranase Glycoside hydrolase family 66
KeywordsHYDROLASE / glycoside hydrolase / GH66 / dextran / TIM-barrel
Function / homologyGlycosyl hydrolase family 66 / Glycosyl hydrolase family 66 / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / hydrolase activity / Immunoglobulin-like fold / beta-D-glucopyranose / alpha-D-glucopyranose / Candidate dextranase Glycoside hydrolase family 66
Function and homology information
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

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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)65,1425
Polymers64,5791
Non-polymers5634
Water4,738263
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 area140 Å2
ΔGint-13 kcal/mol
Surface area20710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.181, 48.381, 76.487
Angle α, β, γ (deg.)90.000, 104.405, 90.000
Int Tables number5
Space group name H-MC121

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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: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


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
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / 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 / Water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.15 Å3/Da / Density % sol: 42.87 %
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→47.26 Å / Num. obs: 50429 / % possible obs: 98.3 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.083 / Rrim(I) all: 0.156 / Net I/σ(I): 10.3
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.963 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 50429 / CC1/2: 0.854 / Rpim(I) all: 0.591 / Rrim(I) all: 1.133

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→47.256 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.919 / SU B: 9.796 / SU ML: 0.151 / Cross valid method: FREE R-VALUE / ESU R: 0.151 / ESU R Free: 0.149
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2593 2464 4.886 %
Rwork0.2061 47964 -
all0.209 --
obs-50428 98.258 %
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: 27.053 Å2
Baniso -1Baniso -2Baniso -3
1-2.111 Å20 Å21.288 Å2
2---0.833 Å20 Å2
3----1.714 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4353 0 37 263 4653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0124516
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164101
X-RAY DIFFRACTIONr_angle_refined_deg2.1651.6456141
X-RAY DIFFRACTIONr_angle_other_deg0.721.5749442
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9645550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.146510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96710723
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.03310223
X-RAY DIFFRACTIONr_chiral_restr0.1060.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.025286
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021082
X-RAY DIFFRACTIONr_nbd_refined0.2150.2873
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.23928
X-RAY DIFFRACTIONr_nbtor_refined0.1890.22191
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.22360
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2281
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0220.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0930.212
X-RAY DIFFRACTIONr_nbd_other0.2080.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1730.213
X-RAY DIFFRACTIONr_mcbond_it1.0490.922200
X-RAY DIFFRACTIONr_mcbond_other1.0490.922200
X-RAY DIFFRACTIONr_mcangle_it1.5321.6472750
X-RAY DIFFRACTIONr_mcangle_other1.5321.6472751
X-RAY DIFFRACTIONr_scbond_it1.6821.092316
X-RAY DIFFRACTIONr_scbond_other1.6821.0912317
X-RAY DIFFRACTIONr_scangle_it2.5081.9383391
X-RAY DIFFRACTIONr_scangle_other2.5071.9393392
X-RAY DIFFRACTIONr_lrange_it4.48310.0255177
X-RAY DIFFRACTIONr_lrange_other4.4869.4255137
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
1.8-1.8470.3461510.3235180.32137840.8970.91196.96090.289
1.847-1.8970.3451790.29433610.29736270.9080.92797.60130.261
1.897-1.9520.3371900.27532900.27935760.9140.93897.31540.24
1.952-2.0120.3131630.25432070.25734740.9310.94997.00630.218
2.012-2.0780.2791600.24731500.24933650.9410.95398.36550.212
2.078-2.1510.3311660.24530210.2532440.9230.95798.24290.214
2.151-2.2320.2811630.21428810.21731170.9530.96797.6580.183
2.232-2.3230.2781450.20528690.20930760.9550.97197.98440.178
2.323-2.4260.2741450.20726970.2128950.9510.97298.16930.178
2.426-2.5440.2511260.18826160.19127820.9650.97898.56220.16
2.544-2.6810.2821200.19524810.19926320.950.97798.82220.172
2.681-2.8430.2941140.20223660.20625100.9470.97498.80480.181
2.843-3.0390.2751140.20422450.20823830.9510.97298.99290.188
3.039-3.2810.2521110.20420400.20721680.9560.97599.21590.194
3.281-3.5920.204910.17519430.17720470.9770.98499.36490.169
3.592-4.0130.21840.17717600.17818510.9730.98399.62180.174
4.013-4.6290.237810.16515400.16916340.9670.98499.20440.166
4.629-5.6550.204760.17313220.17414040.9760.98599.57260.174
5.655-7.9410.166500.1710440.1710970.9810.98499.72650.169
7.941-47.2560.17350.166130.166530.9820.98699.23430.176
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)
11.4150.81820.04152.9635-0.94231.96320.0388-0.1525-0.08640.14230.09670.39640.1645-0.2752-0.13550.3742-0.00290.00310.06910.02930.0913-41.086-40.238-24.686
22.07710.97840.34731.58910.05430.7801-0.0296-0.0973-0.18350.1531-0.0289-0.35240.17110.1370.05850.3540.0334-0.05090.04970.0170.0887-11.155-31.786-17.366
31.55010.0025-0.13843.5357-1.66552.3196-0.0815-0.12110.31490.3317-0.0593-0.5739-0.33870.43320.14070.265-0.0061-0.12690.18480.00910.26480.469-16.236-18.682
41.18970.0834-0.35831.0157-0.28761.1414-0.0374-0.0540.16520.1416-0.0212-0.032-0.04940.04310.05860.32630.0059-0.04760.0035-0.00530.0382-24.839-17.701-16.785
51.41560.50340.56531.61670.60452.6907-0.01480.03310.0022-0.0043-0.01070.4019-0.1363-0.43580.02550.36910.03020.00780.08460.01040.1152-48.427-18.91-15.797
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA38 - 128
2X-RAY DIFFRACTION2ALLA129 - 228
3X-RAY DIFFRACTION3ALLA229 - 287
4X-RAY DIFFRACTION4ALLA288 - 481
5X-RAY DIFFRACTION5ALLA482 - 586

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