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- PDB-6y0x: Fucosylated antimicrobial peptide SB6 in complex with the lectin ... -

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Basic information

Entry
Database: PDB / ID: 6y0x
TitleFucosylated antimicrobial peptide SB6 in complex with the lectin LecRSL from Ralstonia solanacearum at 2.4 Angstrom resolution
Components
  • (SB6) x 2
  • Fucose-binding lectin protein
KeywordsANTIBIOTIC / Antimicrobial / Linear / Lectin
Function / homology
Function and homology information


carbohydrate binding / metal ion binding
Similarity search - Function
Lipocalin - #190 / Fucose-specific lectin / Fungal fucose-specific lectin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
D-LYSINE / Chem-ZDC / polypeptide(D) / polypeptide(D) (> 10) / Fucose-binding lectin protein
Similarity search - Component
Biological speciesRalstonia solanacearum (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.425 Å
AuthorsBaeriswyl, S. / Stocker, A. / Reymond, J.-L.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: To Be Published
Title: Fucosylated antimicrobial peptide SB6 in complex with the lectin LecRSL from Ralstonia solanacearum at 2.4 Angstrom resolution
Authors: Baeriswyl, S. / Stocker, A. / Reymond, J.-L.
History
DepositionFeb 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fucose-binding lectin protein
B: Fucose-binding lectin protein
I: SB6
J: SB6
C: Fucose-binding lectin protein
K: SB6
L: SB6
D: Fucose-binding lectin protein
M: SB6
E: Fucose-binding lectin protein
O: SB6
F: Fucose-binding lectin protein
Q: SB6
R: SB6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,25427
Polymers70,63314
Non-polymers2,62113
Water1,69394
1
A: Fucose-binding lectin protein
B: Fucose-binding lectin protein
I: SB6
J: SB6
C: Fucose-binding lectin protein
K: SB6
L: SB6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,70114
Polymers35,3187
Non-polymers1,3837
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Fucose-binding lectin protein
M: SB6
E: Fucose-binding lectin protein
O: SB6
F: Fucose-binding lectin protein
Q: SB6
R: SB6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,55313
Polymers35,3167
Non-polymers1,2376
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.510, 100.510, 271.653
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11Q-201-

HOH

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Components

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Polypeptide(D) , 2 types, 8 molecules IKRJLMOQ

#2: Polypeptide(D) SB6


Mass: 1431.855 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: Fucosylated linear antimicrobial peptide SB6 incomplete
Source: (synth.) synthetic construct (others)
#3: Polypeptide(D)
SB6


Mass: 1429.863 Da / Num. of mol.: 5 / Source method: obtained synthetically
Details: Fucosylated linear antimicrobial peptide SB6 incomplete
Source: (synth.) synthetic construct (others)

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Protein / Sugars , 2 types, 18 molecules ABCDEF

#1: Protein
Fucose-binding lectin protein / Putative fucose-binding lectin protein


Mass: 9864.758 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria)
Gene: E7Z57_08365, RSP795_21825, RSP822_19650, RUN39_v1_50103
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0S4TLR1
#4: Sugar
ChemComp-ZDC / 3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid


Type: D-saccharide / Mass: 206.193 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C8H14O6 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 2 types, 95 molecules

#5: Chemical ChemComp-DLY / D-LYSINE


Type: D-peptide linking / Mass: 146.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14N2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 4.81 Å3/Da / Density % sol: 74.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000031 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 6, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000031 Å / Relative weight: 1
ReflectionResolution: 2.425→49.1 Å / Num. obs: 100762 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 62.286 Å2 / CC1/2: 0.991 / Rrim(I) all: 0.382 / Χ2: 1 / Net I/σ(I): 2.39
Reflection shellResolution: 2.425→2.437 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1.01 / Num. unique obs: 16188 / CC1/2: 0.39 / Rrim(I) all: 3.369 / % possible all: 99.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.17 Å49.1 Å
Translation7.17 Å49.1 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASER2.7.16phasing
PHENIXv1.11.1-2575refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AJC

5ajc


Resolution: 2.425→49.1 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.25 / Phase error: 33.53
RfactorNum. reflection% reflection
Rfree0.2798 5064 5.04 %
Rwork0.2427 --
obs0.2446 100558 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 144.05 Å2 / Biso mean: 75.186 Å2 / Biso min: 25.8 Å2
Refinement stepCycle: final / Resolution: 2.425→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4619 0 180 94 4893
Biso mean--78.55 51.68 -
Num. residues----610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084975
X-RAY DIFFRACTIONf_angle_d1.0456785
X-RAY DIFFRACTIONf_chiral_restr0.06783
X-RAY DIFFRACTIONf_plane_restr0.005796
X-RAY DIFFRACTIONf_dihedral_angle_d12.8172483
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.425-2.45230.41661650.3701313296
2.4523-2.48120.41091630.35513125100
2.4812-2.51140.37091660.36173214100
2.5114-2.54320.40091690.33583177100
2.5432-2.57670.38961710.32813230100
2.5767-2.6120.34451670.33383149100
2.612-2.64930.37871670.31093219100
2.6493-2.68880.33911680.3143195100
2.6888-2.73080.35761660.36893169100
2.7308-2.77560.45551710.36043207100
2.7756-2.82350.43141690.35093157100
2.8235-2.87480.3811620.33483204100
2.8748-2.93010.37621710.29373158100
2.9301-2.98990.37741700.2763200100
2.9899-3.05490.3021710.25273206100
3.0549-3.12590.29781680.23193191100
3.1259-3.20410.25161680.22983174100
3.2041-3.29070.32191640.23223197100
3.2907-3.38750.2941720.20553172100
3.3875-3.49680.28411730.20453181100
3.4968-3.62180.30191670.20443204100
3.6218-3.76670.21551630.20223183100
3.7667-3.93810.25431720.19543194100
3.9381-4.14560.2661660.19553192100
4.1456-4.40520.22691710.21733185100
4.4052-4.74510.21221710.2093316899
4.7451-5.22210.20341710.22513165100
5.2221-5.97660.23911770.21183185100
5.9766-7.52560.25451740.2393189100
7.5256-49.10.271710.2816317299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.2614-1.66251.18735.6557-5.65945.667-0.7484-0.1090.34710.4310.0847-1.485-0.3961-0.05220.5870.7917-0.0529-0.00280.7471-0.12110.5591-18.307341.6871-25.4027
23.87610.23490.56040.5645-0.25472.0607-0.4735-0.14210.15740.44010.5560.5314-0.4783-2.1318-0.03410.66390.0899-0.12461.4345-0.07640.4747-22.346835.9741-24.7953
37.50715.46684.4165.91364.93987.6217-0.2683-0.83510.5057-0.3414-0.43131.0359-0.3509-1.76930.67370.68660.0835-0.14091.1291-0.20030.6348-27.681739.1246-25.7062
45.30541.9155-2.58816.3079-1.09215.8331-0.42661.08440.6693-1.74530.55622.1933-0.6178-2.1976-0.22930.75220.2558-0.19631.3317-0.27340.9091-26.058847.4228-17.7757
55.2515-0.90781.22965.76561.25211.53690.1726-0.50920.24070.151-0.70470.24980.6032-0.32360.63670.736-0.1457-0.11120.9879-0.0450.5358-17.488434.686-15.861
66.3543.0891-0.64189.7290.60985.05580.1787-0.90570.50460.9983-0.20250.4763-0.4804-1.66550.01180.56750.1884-0.09511.234-0.15510.588-19.647342.7468-12.5964
74.6608-0.9307-1.08052.10113.89456.94440.0072-0.79180.98951.12340.12840.64290.4185-0.627-0.16960.63360.08980.02821.6692-0.22760.745-21.097741.9321-7.789
83.88211.92961.63542.66932.75816.3959-0.5051-0.78240.2776-0.24080.4731-0.3101-0.9458-1.0277-0.03370.49460.1326-0.00460.8253-0.17480.4528-9.614641.4485-13.7649
95.48081.9293-0.87154.8771-5.7947.1415-0.0951-0.7530.95291.07340.27880.6408-1.4453-0.57860.01430.84290.09260.05940.7173-0.27120.553-5.176346.7058-10.8958
105.61121.2413-4.68592.19620.70385.92660.0107-1.30660.0505-0.5809-0.15050.13910.756-0.23750.22670.60480.1429-0.00591.2406-0.01310.4665-6.492140.0613-4.498
115.1818-5.76010.43817.8892-1.2230.4026-0.0172-2.12382.2341-0.32360.4616-0.26560.7052-0.5658-0.34530.8638-0.0284-0.16010.5451-0.07720.63320.945150.4261-17.6351
124.79551.88940.33052.43692.08052.3094-0.1891-0.1917-0.28060.62860.19571.0477-0.84250.50470.06570.6837-0.03490.01840.74410.01750.4673-4.12534.0856-18.7847
134.51551.3958-0.42245.71780.34320.0413-0.4682-0.18760.2022-0.34210.235-0.37050.0260.30630.14960.71920.0204-0.05020.643-0.05030.41851.136540.8204-21.2052
144.6474.8484-4.17328.6967-4.68223.7605-0.44290.0574-0.3015-0.50360.3567-0.4617-0.316-0.58130.20260.41430.0307-0.03540.6372-0.10860.4545.415438.7964-21.968
155.5499-0.2787-2.56763.9757-4.22156.2175-0.1884-0.3590.3858-0.08750.60870.364-0.7124-0.788-0.36980.53760.0744-0.21170.59940.02940.5825-6.598341.2451-27.7094
162.85561.0584-1.6488.03982.1321.98340.03270.22780.2495-0.41330.0736-0.4075-0.18630.1128-0.12870.4858-0.0251-0.0750.566-0.00740.491-3.821737.7233-32.1788
172.4152-3.28222.675.9985-4.87124.0869-0.4345-0.3923-0.5490.20.34980.2322-0.47270.22770.26710.54710.0457-0.08030.6127-0.0140.60780.395133.2096-34.9622
186.3751-4.1008-3.95843.17882.82922.5994-1.6271-0.6831-0.07081.38870.74640.2115-2.7230.72270.95520.98110.1767-0.21950.63530.10770.7307-11.807245.146-39.1243
194.06240.43932.05850.41261.4865.2304-0.0853-0.19550.1017-0.62320.28270.6816-0.0348-0.7275-0.26410.44020.0678-0.03170.69320.06640.3826-14.386933.464-30.6311
205.1263-0.89932.52483.0653-0.57985.68390.37550.4657-0.1234-0.6404-0.4291.0081-0.4476-0.92340.02790.48640.1436-0.04530.7535-0.06510.442-19.093636.8827-36.8625
214.4144-4.7205-4.94257.06384.81336.82781.0078-0.4133-0.4646-1.1380.04240.53730.0602-0.7919-0.81220.6202-0.13710.00780.46680.0960.466915.75145.277610.7999
223.28460.5250.25556.8913-2.57141.91570.0625-1.0018-0.4250.34110.8086-0.7125-0.19940.7317-0.790.4331-0.1269-0.03460.6022-0.03440.426618.86239.418913.0068
235.4272-0.8840.57064.203-4.4364.64880.2164-0.34180.0619-0.31370.16970.2788-0.4329-0.6265-0.35850.5651-0.02970.04940.576-0.05830.356316.642840.166519.0521
247.3886-5.53897.47245.1905-5.57077.55380.4614-0.56010.7235-1.6547-0.4752-0.04290.1185-0.65390.04860.90650.10970.02010.5554-0.11010.429917.942253.428120.9831
252.7938-1.0581-0.48544.53073.88324.1435-0.091-0.44020.2277-0.31490.4004-0.1629-0.54090.4426-0.40350.6897-0.00980.01090.528-0.00970.341726.689248.746413.6118
264.4863.9027-2.51019.9421.99084.1261-0.01210.0298-0.1508-0.84970.3176-0.469-1.15511.0253-0.31870.4843-0.1288-0.07580.6732-0.02830.571130.460746.428321.3635
275.0228-3.23631.93776.42122.44374.4596-0.2224-1.59251.1617-0.4357-0.17771.5279-2.6982-0.37230.13660.875-0.12540.01150.4649-0.12630.855630.904159.984512.721
284.6164-3.5081-4.09498.23884.65225.69610.33430.0742-0.0739-1.1181-0.21640.4858-0.78430.0905-0.31420.6506-0.0308-0.01840.5557-0.00320.535422.840353.86146.2495
295.0847-2.92341.80073.1827-2.32216.46630.5730.08930.75610.0888-0.5273-0.5608-0.29210.3285-0.03890.6031-0.1253-0.0130.441-0.05750.453228.32656.51114.2448
305.4622-1.1624.56923.1545-1.78169.2383-0.401-0.06560.8409-0.18170.1278-0.5657-0.37460.18190.19940.6602-0.20370.00070.6226-0.0170.547734.761957.78284.0015
315.3535-5.4974-0.45886.69080.12755.61250.05270.38350.1610.1761-0.2751-0.151-0.0270.0880.23810.6327-0.055-0.040.4558-0.05670.429824.222452.2682-2.9132
324.145-0.1097-0.00182.0243-2.65533.41390.46480.54580.40340.0384-0.16830.0214-0.2933-0.1422-0.29060.80060.00980.00470.4675-0.03340.479921.26953.7568-6.5691
331.9530.9821-2.53524.9252-2.13274.09920.73750.12460.7123-0.526-0.12510.4098-0.13720.0605-0.5370.7886-0.01720.00370.66770.00110.519622.01453.728-11.6094
345.985-2.0833-0.47293.55341.93246.01750.42940.28350.1809-0.4108-0.174-0.0021-0.4786-0.8011-0.31210.46180.03460.04270.52020.02340.32613.547545.4999-4.1552
358.49312.8714-3.585.4065-3.18142.37380.7967-0.1736-0.62940.6595-0.7669-0.0152-0.5574-0.0873-0.08370.7414-0.0876-0.06950.6177-0.04430.453913.14141.2837-11.4127
368.90852.8051.45937.7383-6.47357.25720.10281.07960.66541.44050.030.8115-1.1351-1.2927-0.37360.68540.09080.04960.6852-0.17640.60892.638944.43112.468
378.3515-2.67925.14035.5163-5.02016.0514-0.9958-0.11890.23411.31580.4503-0.42330.1289-0.19220.65230.5003-0.07610.05850.50240.02580.332618.4537.54222.3651
381.0365-0.9050.53018.8010.620.4602-0.324-0.2811-0.5021-0.70310.44270.739-0.4567-0.0383-0.1450.59540.0042-0.09340.5731-0.02450.38512.970437.97534.2795
395.5413-0.5332.06817.4231-1.58432.1608-0.106-0.0090.2708-1.66990.08580.2817-1.2902-1.0321-0.02510.6166-0.1035-0.00830.743-0.11430.38037.514538.94667.5314
406.3911-3.6981-5.42783.10192.4475.5032-0.1563-0.2974-1.066-0.1446-0.43260.3824-0.2542-0.03840.35570.6038-0.0331-0.17190.7354-0.01190.61258.438831.3730.822
413.54972.5090.15552.5418-2.06776.16040.4156-1.94930.2812-1.39040.17590.3665-3.1972.1403-0.58780.7442-0.1620.05460.7963-0.06080.45648.963636.784715.5305
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )A1 - 10
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 22 )A11 - 22
3X-RAY DIFFRACTION3chain 'A' and (resid 23 through 38 )A23 - 38
4X-RAY DIFFRACTION4chain 'A' and (resid 39 through 46 )A39 - 46
5X-RAY DIFFRACTION5chain 'A' and (resid 47 through 57 )A47 - 57
6X-RAY DIFFRACTION6chain 'A' and (resid 58 through 76 )A58 - 76
7X-RAY DIFFRACTION7chain 'A' and (resid 77 through 89 )A77 - 89
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 22 )B1 - 22
9X-RAY DIFFRACTION9chain 'B' and (resid 23 through 31 )B23 - 31
10X-RAY DIFFRACTION10chain 'B' and (resid 32 through 41 )B32 - 41
11X-RAY DIFFRACTION11chain 'B' and (resid 42 through 46 )B42 - 46
12X-RAY DIFFRACTION12chain 'B' and (resid 47 through 57 )B47 - 57
13X-RAY DIFFRACTION13chain 'B' and (resid 58 through 76 )B58 - 76
14X-RAY DIFFRACTION14chain 'B' and (resid 77 through 89 )B77 - 89
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 10 )C1 - 10
16X-RAY DIFFRACTION16chain 'C' and (resid 11 through 31 )C11 - 31
17X-RAY DIFFRACTION17chain 'C' and (resid 32 through 41 )C32 - 41
18X-RAY DIFFRACTION18chain 'C' and (resid 42 through 46 )C42 - 46
19X-RAY DIFFRACTION19chain 'C' and (resid 47 through 67 )C47 - 67
20X-RAY DIFFRACTION20chain 'C' and (resid 68 through 89 )C68 - 89
21X-RAY DIFFRACTION21chain 'D' and (resid 1 through 10 )D1 - 10
22X-RAY DIFFRACTION22chain 'D' and (resid 11 through 22 )D11 - 22
23X-RAY DIFFRACTION23chain 'D' and (resid 23 through 41 )D23 - 41
24X-RAY DIFFRACTION24chain 'D' and (resid 42 through 46 )D42 - 46
25X-RAY DIFFRACTION25chain 'D' and (resid 47 through 76 )D47 - 76
26X-RAY DIFFRACTION26chain 'D' and (resid 77 through 83 )D77 - 83
27X-RAY DIFFRACTION27chain 'D' and (resid 84 through 89 )D84 - 89
28X-RAY DIFFRACTION28chain 'E' and (resid 1 through 10 )E1 - 10
29X-RAY DIFFRACTION29chain 'E' and (resid 11 through 31 )E11 - 31
30X-RAY DIFFRACTION30chain 'E' and (resid 32 through 41 )E32 - 41
31X-RAY DIFFRACTION31chain 'E' and (resid 42 through 57 )E42 - 57
32X-RAY DIFFRACTION32chain 'E' and (resid 58 through 76 )E58 - 76
33X-RAY DIFFRACTION33chain 'E' and (resid 77 through 89 )E77 - 89
34X-RAY DIFFRACTION34chain 'F' and (resid 1 through 31 )F1 - 31
35X-RAY DIFFRACTION35chain 'F' and (resid 32 through 41 )F32 - 41
36X-RAY DIFFRACTION36chain 'F' and (resid 42 through 46 )F42 - 46
37X-RAY DIFFRACTION37chain 'F' and (resid 47 through 57 )F47 - 57
38X-RAY DIFFRACTION38chain 'F' and (resid 58 through 67 )F58 - 67
39X-RAY DIFFRACTION39chain 'F' and (resid 68 through 76 )F68 - 76
40X-RAY DIFFRACTION40chain 'F' and (resid 77 through 83 )F77 - 83
41X-RAY DIFFRACTION41chain 'F' and (resid 84 through 89 )F84 - 89

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