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- PDB-7c3d: Crystal structure of AofleA from Arthrobotrys oligospora in compl... -

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Basic information

Entry
Database: PDB / ID: 7c3d
TitleCrystal structure of AofleA from Arthrobotrys oligospora in complex with D-arabinose
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 / alpha-D-arabinopyranose / beta-D-arabinopyranose / Uncharacterized protein
Function and homology information
Biological speciesArthrobotrys oligospora
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.596 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 12, 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)80,50017
Polymers78,9442
Non-polymers1,55615
Water16,376909
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-30 kcal/mol
Surface area24720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.707, 79.054, 135.066
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-SEJ / beta-D-arabinopyranose / beta-D-arabinose / D-arabinose / arabinose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DArapbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-arabinopyranoseCOMMON NAMEGMML 1.0
b-D-ArapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-64K / alpha-D-arabinopyranose / alpha-D-arabinose / D-arabinose / arabinose


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DArapaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-arabinopyranoseCOMMON NAMEGMML 1.0
a-D-ArapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 909 / 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: 2.46 Å3/Da / Density % sol: 49.97 %
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: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.596→50 Å / Num. obs: 101891 / % possible obs: 98.1 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.027 / Rrim(I) all: 0.073 / Χ2: 0.98 / Net I/σ(I): 7.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.667.50.7599600.8290.2910.8050.89897.1
1.66-1.727.40.53100180.9020.2070.570.91397.8
1.72-1.87.20.364100700.9480.1450.3920.94297.9
1.8-1.97.40.2499360.9760.0940.2581.01396.8
1.9-2.027.60.158101430.9890.0610.1691.01298.4
2.02-2.177.20.114101700.9920.0450.1231.03598.5
2.17-2.397.50.088101640.9950.0340.0951.04398
2.39-2.747.40.069103440.9970.0270.0741.04499.2
2.74-3.457.50.052103410.9980.020.0561.04598.5
3.45-507.10.042107450.9980.0170.0450.84899

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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: 1.596→49.752 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1798 5073 4.98 %
Rwork0.1504 96751 -
obs0.1519 101824 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.02 Å2 / Biso mean: 23.0874 Å2 / Biso min: 11.9 Å2
Refinement stepCycle: final / Resolution: 1.596→49.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5420 0 126 909 6455
Biso mean--29.06 33.56 -
Num. residues----689
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.61370.26831530.2524286688
1.6137-1.63270.27731760.2362313597
1.6327-1.65260.26451740.2202317597
1.6526-1.67360.26261430.222320698
1.6736-1.69560.23221820.2055317798
1.6956-1.71880.29371800.2125316998
1.7188-1.74340.21911540.1969320498
1.7434-1.76940.21021540.182318998
1.7694-1.7970.20191610.1786324798
1.797-1.82650.18831590.1653305194
1.8265-1.8580.19761500.1672321198
1.858-1.89180.18641670.1613321898
1.8918-1.92820.21111720.161320298
1.9282-1.96750.19711610.1596326099
1.9675-2.01030.19131710.1533319798
2.0103-2.05710.17831650.154324899
2.0571-2.10850.162040.1469320699
2.1085-2.16550.19451740.1549321698
2.1655-2.22930.17631910.1538312596
2.2293-2.30120.20051670.1541326299
2.3012-2.38350.18751810.1556325699
2.3835-2.47890.21011750.1562327499
2.4789-2.59170.18341590.1489329199
2.5917-2.72830.15411640.1503329799
2.7283-2.89920.16241820.1538319796
2.8992-3.12310.18241570.15093310100
3.1231-3.43730.14171820.13663341100
3.4373-3.93450.16161760.12363350100
3.9345-4.95630.15451700.1111335698
4.9563-49.750.17611690.1568351599

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