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

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Basic information

Entry
Database: PDB / ID: 8iub
TitleCrystal structure of GH66 endodextranase from Flavobacterium johnsoniae in complex with isomaltotriose
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 / Candidate dextranase Glycoside hydrolase family 66
Function and homology information
Biological speciesFlavobacterium johnsoniae UW101 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 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)65,2486
Polymers64,5791
Non-polymers6695
Water9,728540
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 area190 Å2
ΔGint-14 kcal/mol
Surface area20750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.911, 91.058, 137.354
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a6-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 2.03 Å3/Da / Density % sol: 39.39 %
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: May 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.18→45.78 Å / Num. obs: 173012 / % possible obs: 99.9 % / Redundancy: 12.5 % / CC1/2: 1 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.019 / Rrim(I) all: 0.069 / Net I/σ(I): 19
Reflection shellResolution: 1.18→1.2 Å / Rmerge(I) obs: 0.975 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 173012 / CC1/2: 0.804 / Rpim(I) all: 0.302 / Rrim(I) all: 1.065

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.18→45.57 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.542 / SU ML: 0.031 / Cross valid method: FREE R-VALUE / ESU R: 0.04 / ESU R Free: 0.04
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1896 8674 5.016 %
Rwork0.1626 164236 -
all0.164 --
obs-172910 99.81 %
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: 14.527 Å2
Baniso -1Baniso -2Baniso -3
1--0.318 Å2-0 Å20 Å2
2--0.528 Å2-0 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.18→45.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4341 0 42 540 4923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0124542
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164122
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.6446182
X-RAY DIFFRACTIONr_angle_other_deg0.5671.5749498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2685557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.228510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32810731
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.56810223
X-RAY DIFFRACTIONr_chiral_restr0.0860.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025335
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021089
X-RAY DIFFRACTIONr_nbd_refined0.250.2870
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.23926
X-RAY DIFFRACTIONr_nbtor_refined0.1870.22254
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22377
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2379
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0330.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0760.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1040.28
X-RAY DIFFRACTIONr_nbd_other0.1580.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.180.228
X-RAY DIFFRACTIONr_mcbond_it0.4740.6482213
X-RAY DIFFRACTIONr_mcbond_other0.4740.6482213
X-RAY DIFFRACTIONr_mcangle_it0.6961.1672775
X-RAY DIFFRACTIONr_mcangle_other0.6961.1672776
X-RAY DIFFRACTIONr_scbond_it0.5520.7662329
X-RAY DIFFRACTIONr_scbond_other0.5490.7642326
X-RAY DIFFRACTIONr_scangle_it0.7741.3583407
X-RAY DIFFRACTIONr_scangle_other0.771.3543402
X-RAY DIFFRACTIONr_lrange_it1.2638.5615360
X-RAY DIFFRACTIONr_lrange_other1.1976.9685237
X-RAY DIFFRACTIONr_rigid_bond_restr3.33938664
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
1.18-1.2110.275970.232119470.233126630.9450.9699.06030.214
1.211-1.2440.2365880.218117140.219123630.9560.96599.50660.198
1.244-1.280.2366390.203113530.204120420.9580.96999.58480.183
1.28-1.3190.2246020.19110670.192117140.9630.97499.61580.169
1.319-1.3620.2195670.175107170.177113050.9650.97899.81420.154
1.362-1.410.1975290.168104300.169109720.9720.9899.88150.146
1.41-1.4630.1955830.16399950.165105860.9720.98199.92440.141
1.463-1.5230.1884910.15197090.153102030.9750.98499.97060.131
1.523-1.5910.2014690.15193380.15398070.9710.9841000.132
1.591-1.6680.1754900.14489220.14694130.9790.98599.98940.128
1.668-1.7580.1974460.14784820.1589280.9720.9851000.132
1.758-1.8650.184520.15379950.15484470.9780.9841000.139
1.865-1.9930.1823800.15576360.15680160.9750.9841000.145
1.993-2.1530.183780.16170480.16274270.9780.98399.98650.153
2.153-2.3580.1933320.16265520.16468860.9760.98199.9710.157
2.358-2.6350.1823170.16459390.16562570.9760.98199.9840.163
2.635-3.0410.1843060.16652430.16755490.9780.9811000.168
3.041-3.720.1882240.15744970.15947210.9760.9841000.168
3.72-5.2440.1721780.14435600.14637390.9810.98899.97330.162
5.244-45.570.1581060.17420930.17421990.9870.9811000.192
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)
11.4980.233-0.02422.516-0.21482.4578-0.03080.26710.0147-0.54770.0421-0.0758-0.27150.1633-0.01130.1875-0.0185-0.00670.08910.00420.076-7.59234.1368-51.7952
20.3822-0.0156-0.04150.75790.35791.0095-0.0254-0.0021-0.08970.01310.01720.02640.03380.02060.00820.00270.00150.00750.01560.01650.07460.80418.0762-30.162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA41 - 116
2X-RAY DIFFRACTION2ALLA117 - 586

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