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- PDB-7c39: Crystal structure of AofleA from Arthrobotrys oligospora in compl... -

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Basic information

Entry
Database: PDB / ID: 7c39
TitleCrystal structure of AofleA from Arthrobotrys oligospora in complex with methylated L-fucose
ComponentsAoflcA
KeywordsSUGAR BINDING PROTEIN / nematode-trapping fungi / Arthrobotrys oligospora / Fucose-specific Lectin
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / CITRIC ACID / methyl alpha-L-fucopyranoside / Uncharacterized protein
Function and homology information
Biological speciesArthrobotrys oligospora
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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

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Assembly

Deposited unit
A: AoflcA
B: AoflcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,49011
Polymers78,9442
Non-polymers1,5459
Water14,862825
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-19 kcal/mol
Surface area26270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.832, 77.103, 136.841
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 AoflcA


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 (E. coli) / References: UniProt: G1XA82
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Sugar
ChemComp-MFU / methyl alpha-L-fucopyranoside / ALPHA-L-METHYL-FUCOSE / methyl 6-deoxy-alpha-L-galactopyranoside / methyl alpha-L-fucoside / methyl L-fucoside / methyl fucoside / Methyl group


Type: L-saccharide / Mass: 178.183 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C7H14O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-L-fucopyranoseCOMMON NAMEGMML 1.0
o1-methyl-a-L-fucoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 825 / 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: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.4 / Details: 0.1 M sodium citrate pH 4.4 and 30% (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: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 68886 / % possible obs: 99.1 % / Redundancy: 6 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.044 / Rrim(I) all: 0.109 / Χ2: 1.024 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.923.90.80664260.6950.4340.9210.97493.9
1.92-1.995.30.57367390.8470.2690.6360.98698.7
1.99-2.086.70.40769080.9380.1720.4420.98999.9
2.08-2.196.80.31468400.9610.1310.341.012100
2.19-2.336.60.23169060.9740.0970.2511.037100
2.33-2.516.10.17368960.9830.0750.1891.05399.8
2.51-2.766.60.12269290.9920.0510.1321.08799.9
2.76-3.166.40.08869540.9950.0380.0961.05899.8
3.16-3.995.70.06270050.9960.0280.0681.02499.6
3.99-505.50.05172830.9970.0230.0560.97899.6

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Processing

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

7c37


Resolution: 1.85→42.42 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1849 3493 5.08 %
Rwork0.1525 65316 -
obs0.1541 68809 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.3 Å2 / Biso mean: 28.2816 Å2 / Biso min: 10.87 Å2
Refinement stepCycle: final / Resolution: 1.85→42.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5425 0 104 825 6354
Biso mean--37.18 39.97 -
Num. residues----690
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.85-1.86940.27181070.2323204878
1.8694-1.89610.2531250.2189249494
1.8961-1.92440.2691160.211250996
1.9244-1.95450.26021300.1865257598
1.9545-1.98650.20691550.1737259499
1.9865-2.02080.20041430.16292615100
2.0208-2.05750.22591530.16492607100
2.0575-2.09710.2091600.15842601100
2.0971-2.13990.22611250.15492613100
2.1399-2.18640.20471380.15672630100
2.1864-2.23730.21531240.15052677100
2.2373-2.29320.2041470.14872618100
2.2932-2.35520.19641340.14532634100
2.3552-2.42450.18841520.14332626100
2.4245-2.50280.16931470.15072613100
2.5028-2.59220.1821250.15072643100
2.5922-2.6960.19731590.14792649100
2.696-2.81860.18011400.16012652100
2.8186-2.96720.21491140.15712693100
2.9672-3.15310.18531380.15482650100
3.1531-3.39640.16691650.14842646100
3.3964-3.7380.16451640.145264399
3.738-4.27850.15721350.12992720100
4.2785-5.38870.14851380.12992735100
5.3887-42.420.18021590.1664283199
Refinement TLS params.Method: refined / Origin x: -21.8763 Å / Origin y: 2.4662 Å / Origin z: -13.8042 Å
111213212223313233
T0.1514 Å2-0.0105 Å2-0.0096 Å2-0.1303 Å2-0.0017 Å2--0.1522 Å2
L0.7709 °20.3329 °2-0.0412 °2-0.6357 °2-0.0459 °2--0.8754 °2
S-0.066 Å °0.0891 Å °0.0662 Å °-0.0927 Å °0.0569 Å °0.0602 Å °-0.1115 Å °0.0309 Å °0.0007 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 401
2X-RAY DIFFRACTION1allB2 - 401
3X-RAY DIFFRACTION1allC1 - 6
4X-RAY DIFFRACTION1allD4
5X-RAY DIFFRACTION1allS1 - 825

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