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- PDB-7c37: Crystal structure of AofleA from Arthrobotrys oligospora -

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Basic information

Entry
Database: PDB / ID: 7c37
TitleCrystal structure of AofleA from Arthrobotrys oligospora
ComponentsAofleA
KeywordsSUGAR BINDING PROTEIN / nematode-trapping fungi / Arthrobotrys oligospora / Fucose-specific Lectin
Function / homologyFucose-specific lectin / Fucose-specific lectin / Fungal fucose-specific lectin / 6 Propeller / Neuraminidase / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesArthrobotrys oligospora
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.451 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 / Category: citation
Item: _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: AofleA
B: AofleA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5976
Polymers78,9442
Non-polymers6534
Water22,5011249
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-13 kcal/mol
Surface area25510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.413, 78.949, 136.629
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: Chemical
ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1249 / 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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Sodium formate, 0.1 M Bicine pH 8.5, and 20% (w/v) PEG MME 5,000

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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: Jan 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 140546 / % possible obs: 99.8 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.038 / Rrim(I) all: 0.085 / Χ2: 0.95 / Net I/σ(I): 8.4 / Num. measured all: 692668
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.45-1.550.874139350.690.430.9770.911100
1.5-1.564.90.634138670.7890.3150.710.91599.8
1.56-1.634.70.48139560.8490.2470.5410.92199.9
1.63-1.724.90.339139090.9240.1690.380.9299.9
1.72-1.835.20.229139930.9690.1110.2550.9399.9
1.83-1.975.10.151139780.9840.0740.1690.99499.9
1.97-2.174.90.094140390.9930.0470.1060.98999.7
2.17-2.484.70.071140700.9950.0360.081.00699.9
2.48-3.125.20.048142140.9980.0230.0540.967100
3.12-504.80.037145850.9980.0190.0420.9499.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AGI

4agi


Resolution: 1.451→33.285 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.161 7037 5.01 %
Rwork0.1214 133418 -
obs0.1234 140455 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.2 Å2 / Biso mean: 19.8235 Å2 / Biso min: 9.67 Å2
Refinement stepCycle: final / Resolution: 1.451→33.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5422 0 44 1257 6723
Biso mean--41.88 36.2 -
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 (%)
1.451-1.4670.26662330.2006437499
1.467-1.48430.25072370.19334356100
1.4843-1.50240.25542330.18414469100
1.5024-1.52140.23822460.17464354100
1.5214-1.54140.20682220.15574405100
1.5414-1.56260.20672060.14944437100
1.5626-1.58490.20442220.14114435100
1.5849-1.60850.1832580.13624386100
1.6085-1.63370.19742520.13594404100
1.6337-1.66040.19692040.13234391100
1.6604-1.68910.17682450.11884425100
1.6891-1.71980.17852390.11584396100
1.7198-1.75290.16312410.11744431100
1.7529-1.78860.16232100.11564422100
1.7886-1.82750.16142460.11864445100
1.8275-1.870.1532530.1154385100
1.87-1.91680.17352100.11814461100
1.9168-1.96860.14762280.11154437100
1.9686-2.02650.14142340.10554481100
2.0265-2.09190.15672120.11054458100
2.0919-2.16670.16482470.1097440099
2.1667-2.25340.17122360.12294444100
2.2534-2.3560.15562220.11924488100
2.356-2.48010.14582520.11724428100
2.4801-2.63550.15652250.11634541100
2.6355-2.83890.16092260.11964483100
2.8389-3.12430.16322400.11744495100
3.1243-3.5760.1472370.11414536100
3.576-4.50360.14032390.109453199
4.5036-33.2850.14072820.12994720100

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