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- PDB-7c3e: Crystal structure of R97A/R150A/R203A mutant of AofleA from Arthr... -

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Basic information

Entry
Database: PDB / ID: 7c3e
TitleCrystal structure of R97A/R150A/R203A mutant 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 / Resolution: 2.183 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 / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.name
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
C: AofleA
D: AofleA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,50743
Polymers156,8564
Non-polymers3,65139
Water27,0231500
1
A: AofleA
B: AofleA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,39723
Polymers78,4282
Non-polymers1,97021
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8340 Å2
ΔGint-157 kcal/mol
Surface area25460 Å2
MethodPISA
2
C: AofleA
D: AofleA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,10920
Polymers78,4282
Non-polymers1,68218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7750 Å2
ΔGint-115 kcal/mol
Surface area25810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.962, 102.484, 106.020
Angle α, β, γ (deg.)90.000, 91.430, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 16 or resid 18...
21(chain B and (resid 2 through 16 or resid 18...
31(chain C and (resid 2 through 16 or resid 18...
41(chain D and (resid 2 through 16 or resid 18...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 16 or resid 18...A2 - 16
121(chain A and (resid 2 through 16 or resid 18...A18 - 77
131(chain A and (resid 2 through 16 or resid 18...A79 - 158
141(chain A and (resid 2 through 16 or resid 18...A2 - 346
151(chain A and (resid 2 through 16 or resid 18...A213 - 219
161(chain A and (resid 2 through 16 or resid 18...A221 - 223
171(chain A and (resid 2 through 16 or resid 18...A2
181(chain A and (resid 2 through 16 or resid 18...A2 - 346
191(chain A and (resid 2 through 16 or resid 18...A342 - 345
1101(chain A and (resid 2 through 16 or resid 18...A601 - 901
1111(chain A and (resid 2 through 16 or resid 18...A1101
211(chain B and (resid 2 through 16 or resid 18...B2 - 16
221(chain B and (resid 2 through 16 or resid 18...B18 - 77
231(chain B and (resid 2 through 16 or resid 18...B79 - 15
241(chain B and (resid 2 through 16 or resid 18...B2 - 345
251(chain B and (resid 2 through 16 or resid 18...B213 - 219
261(chain B and (resid 2 through 16 or resid 18...B221 - 223
271(chain B and (resid 2 through 16 or resid 18...B2
281(chain B and (resid 2 through 16 or resid 18...B2 - 345
291(chain B and (resid 2 through 16 or resid 18...B342 - 501
2101(chain B and (resid 2 through 16 or resid 18...B901
311(chain C and (resid 2 through 16 or resid 18...C2 - 16
321(chain C and (resid 2 through 16 or resid 18...C18 - 77
331(chain C and (resid 2 through 16 or resid 18...C79 - 158
341(chain C and (resid 2 through 16 or resid 18...C160 - 179
351(chain C and (resid 2 through 16 or resid 18...C181 - 211
361(chain C and (resid 2 through 16 or resid 18...C213 - 219
371(chain C and (resid 2 through 16 or resid 18...C221 - 223
381(chain C and (resid 2 through 16 or resid 18...C225 - 33
391(chain C and (resid 2 through 16 or resid 18...C601 - 901
3101(chain C and (resid 2 through 16 or resid 18...C1101
411(chain D and (resid 2 through 16 or resid 18...D2 - 16
421(chain D and (resid 2 through 16 or resid 18...D18 - 77
431(chain D and (resid 2 through 16 or resid 18...D79 - 158
441(chain D and (resid 2 through 16 or resid 18...D2 - 345
451(chain D and (resid 2 through 16 or resid 18...D213 - 219
461(chain D and (resid 2 through 16 or resid 18...D221 - 223
471(chain D and (resid 2 through 16 or resid 18...D2
481(chain D and (resid 2 through 16 or resid 18...D2 - 345
491(chain D and (resid 2 through 16 or resid 18...D342 - 501
4101(chain D and (resid 2 through 16 or resid 18...D901

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Components

#1: Protein
AofleA


Mass: 39213.895 Da / Num. of mol.: 4 / Mutation: R97A, R150A, R203A
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1500 / 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: 2.84 Å3/Da / Density % sol: 56.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.8 M Aammonium sulfate, 0.1 M Bis-Tris pH 6.5, and 2% (v/v) PEG MME 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.183→50 Å / Num. obs: 82334 / % possible obs: 91.3 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.084 / Rrim(I) all: 0.148 / Χ2: 1.02 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.282.70.584360.6120.3570.6180.99493.9
2.28-2.372.70.48284050.7230.3460.5970.95193.6
2.37-2.482.60.32382960.8140.2360.4020.95392.7
2.48-2.612.70.24682650.8850.1750.3030.98492.4
2.61-2.772.80.20683670.9230.1420.2521.02792.6
2.77-2.992.80.15682740.9550.1080.1911.06292.2
2.99-3.292.70.10481810.9780.0730.1281.10390.6
3.29-3.762.90.08481380.9860.0560.1011.13690.3
3.76-4.742.80.0680680.9920.0410.0731.04789.2
4.74-502.90.05479040.9940.0360.0650.93486.1

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C37

7c37


Resolution: 2.183→36.837 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2172 4154 5.05 %
Rwork0.1666 78100 -
obs0.1691 82254 90.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.65 Å2 / Biso mean: 24.1295 Å2 / Biso min: 6.71 Å2
Refinement stepCycle: final / Resolution: 2.183→36.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10762 0 231 1500 12493
Biso mean--34.56 31.03 -
Num. residues----1378
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6168X-RAY DIFFRACTION9.034TORSIONAL
12B6168X-RAY DIFFRACTION9.034TORSIONAL
13C6168X-RAY DIFFRACTION9.034TORSIONAL
14D6168X-RAY DIFFRACTION9.034TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.183-2.20770.36541080.2956183264
2.2077-2.23360.33641530.2587265593
2.2336-2.26090.32881270.2698272894
2.2609-2.28950.30391300.2436266693
2.2895-2.31960.29191420.2344265294
2.3196-2.35140.26921180.2087273793
2.3514-2.3850.25681360.2005268793
2.385-2.42060.29581390.1999267193
2.4206-2.45840.25941640.1988263892
2.4584-2.49870.26041360.1808264792
2.4987-2.54170.25431400.1829265992
2.5417-2.58790.26111500.1807262592
2.5879-2.63770.24921290.1761267693
2.6377-2.69150.26371410.1754267893
2.6915-2.750.2251590.1701262392
2.75-2.8140.23131270.1659267192
2.814-2.88430.2171340.1683267292
2.8843-2.96230.24851310.1627264192
2.9623-3.04940.24051470.1669265391
3.0494-3.14780.1991460.1596259390
3.1478-3.26020.19251310.1578258590
3.2602-3.39070.19411670.1517257690
3.3907-3.54490.16511570.1438260191
3.5449-3.73160.18851550.1391256790
3.7316-3.96510.19641250.1395261990
3.9651-4.27090.16891340.1254259989
4.2709-4.69990.12731250.1166256488
4.6999-5.37820.17021170.1295255387
5.3782-6.76910.1881530.1606251987
6.7691-36.830.21041330.1781251385

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