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- PDB-7c38: Crystal structure of AofleA from Arthrobotrys oligospora in compl... -

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Basic information

Entry
Database: PDB / ID: 7c38
TitleCrystal structure of AofleA from Arthrobotrys oligospora in complex with L-fucose
ComponentsAofleA
KeywordsSUGAR BINDING PROTEIN / nematode-trapping fungi / Arthrobotrys oligospora / Fucose-specific Lectin
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / alpha-L-fucopyranose / beta-L-fucopyranose / Uncharacterized protein
Function and homology information
Biological speciesArthrobotrys oligospora
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsLiu, M. / Cheng, X. / Wang, J. / Zhang, M. / Wang, M.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770066 China
Other governmentKJ2019ZD02 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Structural insights into the fungi-nematodes interaction mediated by fucose-specific lectin AofleA from Arthrobotrys oligospora.
Authors: Liu, M. / Cheng, X. / Wang, J. / Tian, D. / Tang, K. / Xu, T. / Zhang, M. / Wang, Y. / Wang, M.
History
DepositionMay 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.2Aug 12, 2020Group: Database references / Structure summary / Category: chem_comp / citation
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 23, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AofleA
B: AofleA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,62614
Polymers78,9442
Non-polymers1,68212
Water22,6991260
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-10 kcal/mol
Surface area26200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.424, 66.938, 209.744
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 AofleA


Mass: 39472.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobotrys oligospora (strain ATCC 24927 / CBS 115.81 / DSM 1491) (fungus)
Strain: ATCC 24927 / CBS 115.81 / DSM 1491 / Gene: AOL_s00076g540 / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: G1XA82
#2: Sugar
ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar
ChemComp-FUL / beta-L-fucopyranose / beta-L-fucose / 6-deoxy-beta-L-galactopyranose / L-fucose / fucose / 6-DEOXY-BETA-L-GALACTOSE


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fucopyranoseCOMMON NAMEGMML 1.0
b-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1260 / 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: 2.24 Å3/Da / Density % sol: 45.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Ssodium citrate pH 5.5 and 22% (w/v) PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 210395 / % possible obs: 94.7 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.03 / Rrim(I) all: 0.075 / Χ2: 1.014 / Net I/σ(I): 14.9 / Num. measured all: 1226269
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.2-1.245.60.212203590.9670.0960.2350.9592.9
1.24-1.295.90.185207600.9740.0810.2030.9794.1
1.29-1.355.80.157207860.980.0690.1720.98194.6
1.35-1.425.60.132206520.9840.060.1461.0293.7
1.42-1.515.70.111205960.9880.0490.1221.04793.3
1.51-1.6360.096210320.9910.0420.1051.08594.9
1.63-1.795.80.083214370.9930.0360.0911.06396.7
1.79-2.055.50.068214700.9950.030.0751.01596.4
2.05-2.596.20.061221280.9960.0250.0660.95998.7
2.59-506.10.054211750.9960.0230.0591.05391.6

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C37

7c37


Resolution: 1.2→27.349 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 11.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1386 10548 5.02 %
Rwork0.1124 199603 -
obs0.1137 210151 94.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.5 Å2 / Biso mean: 14.1833 Å2 / Biso min: 4.56 Å2
Refinement stepCycle: final / Resolution: 1.2→27.349 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5404 0 118 1293 6815
Biso mean--12.66 29.64 -
Num. residues----687
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2-1.21340.14723390.1171622690
1.2134-1.22770.13842860.1045655793
1.2277-1.24270.12863340.1001648594
1.2427-1.25840.14873370.1084656394
1.2584-1.27490.13933400.1064655694
1.2749-1.29240.13223410.1038657393
1.2924-1.31090.13283390.1053659095
1.3109-1.33040.14933590.1042657394
1.3304-1.35120.13793490.1039655695
1.3512-1.37340.13993310.1028655594
1.3734-1.39710.13653640.0991653593
1.3971-1.42250.12643500.0999652694
1.4225-1.44980.13023350.097647192
1.4498-1.47940.13093550.0953654194
1.4794-1.51160.12483480.0946652994
1.5116-1.54670.12363650.093656694
1.5467-1.58540.11493390.0932667795
1.5854-1.62830.13093580.0951673396
1.6283-1.67620.12283580.0982675796
1.6762-1.73030.13253480.106675697
1.7303-1.79210.14613870.108683697
1.7921-1.86390.13273950.1106686797
1.8639-1.94870.14233580.1095662194
1.9487-2.05140.12273630.1085685297
2.0514-2.17980.13543890.115695099
2.1798-2.34810.13873660.1147699599
2.3481-2.58420.14173380.1242709499
2.5842-2.95770.15143960.1233708899
2.9577-3.7250.14163580.1207673893
3.725-27.3490.16243230.1399623783

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