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- PDB-8iu8: Crystal structure of GH66 endodextranase from Flavobacterium john... -

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Basic information

Entry
Database: PDB / ID: 8iu8
TitleCrystal structure of GH66 endodextranase from Flavobacterium johnsoniae
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
Candidate dextranase Glycoside hydrolase family 66
Similarity search - Component
Biological speciesFlavobacterium johnsoniae UW101 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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)64,6712
Polymers64,5791
Non-polymers921
Water6,395355
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 area270 Å2
ΔGint-0 kcal/mol
Surface area20850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.241, 48.409, 76.453
Angle α, β, γ (deg.)90.000, 104.601, 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.17 Å3/Da / Density % sol: 43.22 %
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: 1.85→47.3 Å / Num. obs: 47439 / % possible obs: 99.7 % / Redundancy: 6.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.073 / Rrim(I) all: 0.134 / Net I/σ(I): 10.1
Reflection shellResolution: 1.85→1.89 Å / Rmerge(I) obs: 0.875 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 47439 / CC1/2: 0.87 / Rpim(I) all: 0.546 / Rrim(I) all: 1.033

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→47.3 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.221 / SU ML: 0.115 / Cross valid method: FREE R-VALUE / ESU R: 0.14 / ESU R Free: 0.141
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2304 2332 4.917 %
Rwork0.1748 45096 -
all0.177 --
obs-47428 99.637 %
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: 32.254 Å2
Baniso -1Baniso -2Baniso -3
1-1.714 Å2-0 Å2-0.286 Å2
2---0.5 Å2-0 Å2
3----0.938 Å2
Refinement stepCycle: LAST / Resolution: 1.85→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4341 0 6 355 4702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0114494
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164082
X-RAY DIFFRACTIONr_angle_refined_deg2.1511.6426113
X-RAY DIFFRACTIONr_angle_other_deg0.7481.5749397
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2945554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.722510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.86510724
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.13810224
X-RAY DIFFRACTIONr_chiral_restr0.1130.2650
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.025311
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021086
X-RAY DIFFRACTIONr_nbd_refined0.2190.2854
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.23927
X-RAY DIFFRACTIONr_nbtor_refined0.1930.22216
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.22473
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2332
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1680.29
X-RAY DIFFRACTIONr_nbd_other0.1590.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1680.215
X-RAY DIFFRACTIONr_mcbond_it1.9271.6152204
X-RAY DIFFRACTIONr_mcbond_other1.9261.6152204
X-RAY DIFFRACTIONr_mcangle_it2.5462.8892759
X-RAY DIFFRACTIONr_mcangle_other2.5462.8882760
X-RAY DIFFRACTIONr_scbond_it2.8091.8142290
X-RAY DIFFRACTIONr_scbond_other2.8081.8142291
X-RAY DIFFRACTIONr_scangle_it3.9023.2313353
X-RAY DIFFRACTIONr_scangle_other3.9013.2323354
X-RAY DIFFRACTIONr_lrange_it5.78317.0015234
X-RAY DIFFRACTIONr_lrange_other5.76616.2535174
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
1.85-1.8980.2881700.26733010.26834720.9360.94699.97120.252
1.898-1.950.2431390.21432890.21534290.9590.96599.97080.195
1.95-2.0060.271700.2131330.21333030.9490.9681000.189
2.006-2.0680.2451560.19730340.19931920.960.97399.93730.177
2.068-2.1360.2691580.19729370.20131030.9520.97599.74220.177
2.136-2.210.2421560.17828870.18130480.9620.97999.8360.16
2.21-2.2940.2431480.17727530.18129040.9630.97899.89670.156
2.294-2.3870.2491480.18226720.18628230.9590.97999.89370.16
2.387-2.4930.2571270.17725470.18126790.9610.98199.81340.157
2.493-2.6140.281430.17824100.18325680.9560.98199.41590.162
2.614-2.7550.2531320.17422950.17824460.9630.98299.22320.16
2.755-2.9220.2621210.17822170.18223570.9540.97999.19390.164
2.922-3.1230.247920.18620840.18921850.9610.97799.58810.177
3.123-3.3720.203980.17719330.17820380.9710.98299.65650.174
3.372-3.6920.219930.16417760.16618870.9730.98599.04610.165
3.692-4.1240.184850.1516150.15217230.9770.98698.66510.158
4.124-4.7560.155740.13214360.13315270.9860.9998.88670.142
4.756-5.810.218540.14112210.14412800.980.98999.60940.15
5.81-8.1560.16450.1469850.14710370.9760.98699.3250.157
8.156-47.30.248230.1935710.1955970.9580.97899.49750.21
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)
12.07370.42550.68851.96990.08811.27930.0068-0.1129-0.10540.2167-0.0439-0.0950.11850.09330.03710.23370.02980.04410.02570.01830.0236-22.485-33.273-20.423
21.2557-0.0264-0.4381.2809-0.10171.1837-0.02080.00730.11970.1808-0.00920.0343-0.03980.01690.030.19660.00220.03050.00150.00250.0231-29.188-18.397-16.772
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA39 - 246
2X-RAY DIFFRACTION2ALLA247 - 586

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