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- PDB-6q8g: Structure of Fucosylated D-antimicrobial peptide SB8 in complex w... -

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Basic information

Entry
Database: PDB / ID: 6q8g
TitleStructure of Fucosylated D-antimicrobial peptide SB8 in complex with the Fucose-binding lectin PA-IIL at 1.190 Angstrom resolution
Components
  • Fucose-binding lectin
  • SB8
KeywordsANTIBIOTIC / Antimicrobial / Lectin / Complex
Function / homology
Function and homology information


single-species biofilm formation / carbohydrate binding / metal ion binding
Similarity search - Function
Calcium-mediated lectin / Lectin, sugar-binding / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
AMINO GROUP / Chem-ZDC / polypeptide(D) / polypeptide(D) (> 10) / Fucose-binding lectin / Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.19 Å
AuthorsBaeriswyl, S. / Stocker, A. / Reymond, J.-L.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: X-ray Crystal Structures of Short Antimicrobial Peptides as Pseudomonas aeruginosa Lectin B Complexes.
Authors: Baeriswyl, S. / Gan, B.H. / Siriwardena, T.N. / Visini, R. / Robadey, M. / Javor, S. / Stocker, A. / Darbre, T. / Reymond, J.L.
History
DepositionDec 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fucose-binding lectin
E: SB8
B: Fucose-binding lectin
F: SB8
C: Fucose-binding lectin
G: SB8
D: Fucose-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,87721
Polymers50,7007
Non-polymers1,17714
Water10,611589
1
A: Fucose-binding lectin
E: SB8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3317
Polymers12,9882
Non-polymers3425
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fucose-binding lectin
F: SB8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2515
Polymers12,9882
Non-polymers2623
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fucose-binding lectin
G: SB8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5217
Polymers12,9882
Non-polymers5335
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Fucose-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7752
Polymers11,7351
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.445, 72.085, 123.593
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Polypeptide(D) / Sugars , 3 types, 11 molecules ABCDEFG

#1: Protein
Fucose-binding lectin / Fucose-binding lectin II (PA-IIL) / Fucose-binding lectin PA-IIL


Mass: 11734.707 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Fucose-binding lectin PA-IIL Lectin B from Pseudomonas aeruginosa
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: lecB, C0043_24310, C0044_25260, C0046_23510, CAZ10_21840, CW299_25270, DI492_13230, DT376_00595, PAERUG_E15_London_28_01_14_00983, PAMH19_1713, RW109_RW109_02453
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A069Q9V4, UniProt: Q9HYN5*PLUS
#2: Polypeptide(D) SB8


Mass: 1253.666 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Fucosylated D-antimicrobial peptide SB8 / Source: (synth.) synthetic construct (others)
#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.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H14O6

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Non-polymers , 3 types, 599 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NH2 / AMINO GROUP


Mass: 16.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NH2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / Source method: isolated from a natural source / Formula: H2O

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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: 51.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.8 M Potassium sodium tartrate tetrahydrate, 0.1 M Tris pH 8.5, 0.5% w/v Polyethylene glycol monomethyl ether 5,000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 19, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.19→46.916 Å / Num. obs: 276822 / % possible obs: 88.6 % / Redundancy: 3.01 % / Rrim(I) all: 0.062 / Net I/σ(I): 11.74
Reflection shellResolution: 1.19→1.196 Å / Mean I/σ(I) obs: 0.82 / Num. unique obs: 189

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.89 Å46.92 Å
Translation2.89 Å46.92 Å

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.0phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OXC

1oxc


Resolution: 1.19→46.916 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0.96 / Phase error: 16.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1605 13820 4.99 %
Rwork0.1447 262883 -
obs0.1455 276703 88.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.09 Å2 / Biso mean: 19.3658 Å2 / Biso min: 8.52 Å2
Refinement stepCycle: final / Resolution: 1.19→46.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3442 0 74 589 4105
Biso mean--22.34 32.12 -
Num. residues----478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083536
X-RAY DIFFRACTIONf_angle_d0.9814841
X-RAY DIFFRACTIONf_chiral_restr0.107624
X-RAY DIFFRACTIONf_plane_restr0.006635
X-RAY DIFFRACTIONf_dihedral_angle_d6.531163
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1903-1.20380.3452560.3352977103310
1.2038-1.2180.37411170.35142213233023
1.218-1.23280.35951730.33583509368235
1.2328-1.24840.33523260.30865958628460
1.2484-1.26480.29213910.29767410780175
1.2648-1.28220.31534310.28738461889285
1.2822-1.30050.27374610.26468938939990
1.3005-1.31990.25254950.2339414990996
1.3199-1.34050.2435070.210696071011497
1.3405-1.36250.22255120.196197101022298
1.3625-1.3860.19085140.184997871030199
1.386-1.41120.17515160.1698983210348100
1.4112-1.43840.18125240.1673987010394100
1.4384-1.46770.1585150.1548980410319100
1.4677-1.49960.1695110.1459987510386100
1.4996-1.53450.15555210.1394989010411100
1.5345-1.57290.17035220.1357983110353100
1.5729-1.61540.14145200.1352987810398100
1.6154-1.6630.1485190.1341985610375100
1.663-1.71660.16515180.1342988010398100
1.7166-1.7780.15545200.1293979310313100
1.778-1.84920.15915120.1289987610388100
1.8492-1.93340.14575200.1214983910359100
1.9334-2.03530.12455220.117998001032299
2.0353-2.16280.13585190.12398331035299
2.1628-2.32980.13825140.126398481036299
2.3298-2.56420.15885260.136798151034199
2.5642-2.93520.14655050.136797791028499
2.9352-3.69790.14815150.131198021031799
3.6979-46.95290.15565180.145297981031699
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)
14.13791.0979-1.12791.1391-0.75291.20650.0593-0.1050.15790.1213-0.0243-0.0515-0.10190.0323-0.02680.113-0.0129-0.00040.0988-0.00730.1419-7.6647-0.738933.8221
23.61170.83021.03261.64330.2211.2428-0.04320.12250.2106-0.0750.01190.1167-0.1447-0.00510.03670.09350.0096-0.0060.11950.0280.1064-15.1278-1.845122.6797
34.55453.05113.52082.92951.34863.9588-0.18680.21550.3657-0.20220.00740.0897-0.33750.01710.14640.13020.0189-0.00570.18760.03810.1775-13.92832.76519.4464
41.71350.1457-0.26491.065-0.05920.9719-0.05640.24440.0556-0.14350.02890.0737-0.0517-0.02970.02730.11210.0131-0.02130.13670.02660.1233-15.7464-6.754117.8464
55.63340.61971.3830.36860.3840.58020.0091-0.010.49090.0093-0.06130.0569-0.1696-0.00790.05030.1021-0.008-0.00520.11060.01790.1769-11.49732.985828.8999
60.5893-0.25750.56720.9537-0.37761.0964-0.02360.0217-0.03220.07040.04320.1485-0.0886-0.0944-0.00830.07690.00530.00830.09130.01190.1212-18.3182-7.24930.7853
70.1870.0855-0.38220.4865-0.30120.869-0.0190.0752-0.0751-0.0614-0.0112-0.0011-0.020.01520.02310.07530.0045-0.00630.09380.00920.1174-7.6192-8.473126.136
83.3187-0.35530.81641.3825-0.41651.9113-0.0485-0.0314-0.13940.06470.06290.10840.1143-0.111-0.06020.1025-0.0126-0.00280.1017-0.00980.1256-17.281-26.996330.0514
92.09280.9806-1.34391.3444-0.42141.4509-0.05840.37470.1233-0.13980.0904-0.0070.0417-0.05670.00070.10320.0153-0.00240.1372-0.00220.0977-8.8872-18.196819.3226
102.55110.8019-0.60190.9372-0.16741.5574-0.13680.2531-0.2797-0.14890.0832-0.03550.2417-0.07920.07320.15160.00230.00980.1697-0.04160.1671-11.039-27.932518.1848
113.17330.0979-0.55657.14673.48126.4066-0.06090.19540.1563-0.45880.0868-0.2584-0.32230.296-0.00630.1289-0.01380.01390.1920.02570.1390.0816-12.377916.1439
122.7481.3611-0.84391.3602-1.08112.244-0.12660.3783-0.1645-0.15620.14340.05520.1873-0.218-0.00970.11610.00880.00040.1495-0.03640.1381-17.8444-22.861619.2367
138.06191.9743-3.27251.0676-1.50382.1548-0.29280.1765-0.5657-0.1250.073-0.21210.2206-0.00380.20240.11340.00570.00780.135-0.03790.1722-8.5975-28.494923.5892
140.9959-0.537-0.25913.692.90852.32290.21370.537-0.2002-0.7562-0.1569-0.41140.49310.3280.0230.24630.06690.05310.2017-0.03870.18992.206-29.211820.0754
150.23670.1195-0.42610.5956-0.02431.03770.01780.002-0.00640.0274-0.018-0.04930.02440.06910.0160.08090.0071-0.00580.095-0.00380.1051-7.7389-18.398830.1882
160.06360.20690.17340.85510.1771.1325-0.01070.0470.2465-0.03530.00020.05530.0184-0.08650.03440.06840.0099-0.00710.1148-0.0070.1188-17.3854-17.437724.928
170.71570.2199-0.08484.60671.8662.50810.06140.02180.0650.05790.0451-0.2951-0.13550.2238-0.06530.1407-0.0263-0.03480.12750.0080.1481.5026-12.663844.0025
181.11940.33020.31441.2876-0.250.75750.1389-0.1091-0.14290.3-0.0956-0.19350.04330.0734-0.02740.2366-0.0366-0.06170.12850.02320.1165-3.0797-22.486655.1176
192.1152.195-0.99483.4251-1.04421.65230.1868-0.1906-0.01590.4299-0.2318-0.2839-0.1350.2154-0.01070.2434-0.052-0.06650.15870.0250.1457-0.9265-13.338455.2826
201.01791.5327-0.49133.544-1.95611.80060.0547-0.0289-0.15150.1008-0.1153-0.42170.09260.25140.08850.1849-0.0063-0.06120.13810.01170.16992.6502-22.396348.8985
216.08021.4246-0.85487.2346-3.05488.55360.0115-0.4546-0.43620.36280.1002-0.15710.50910.3810.03960.270.0313-0.08740.18990.02290.2342.144-33.622250.6565
220.71180.05770.27141.1658-0.92370.95670.1060.0123-0.07090.129-0.091-0.04050.06380.03650.00840.1282-0.0103-0.02130.1015-0.00150.1051-8.2521-20.935543.9398
230.8820.16520.20010.0423-0.07291.08310.1156-0.13010.04340.2619-0.12010.179-0.054-0.00460.01460.176-0.0279-0.01370.1054-0.00440.1056-7.0838-12.247850.5983
241.22770.19360.74793.9244-0.58342.30260.13890.0074-0.02040.1092-0.05190.24010.0427-0.155-0.0940.1211-0.0160.03090.1243-0.00710.1391-26.2091-18.187943.3033
251.45970.4426-0.00521.06070.7551.20880.1577-0.2210.1570.2736-0.13760.2181-0.0288-0.12160.02570.2387-0.04580.06720.1338-0.02620.1237-23.3679-13.12155.9063
263.2152-2.7318-2.88993.55913.69724.72690.1436-0.58040.29090.4058-0.0265-0.1153-0.09910.2686-0.13570.3108-0.09360.0340.2048-0.05190.1539-11.1005-5.244261.0096
270.73611.00491.03582.11771.17052.76410.1853-0.23150.08660.3681-0.24640.28320.2288-0.3166-0.00290.218-0.06360.04820.1736-0.02180.1262-23.6246-20.739554.3197
281.55671.68531.18393.99652.78413.30690.1298-0.11330.24850.0119-0.22910.3877-0.179-0.25770.09120.1977-0.01850.07060.1294-0.02760.1769-27.2557-10.244450.7505
292.90750.1060.2981.98530.48116.81880.1349-0.56620.26720.5538-0.07120.336-0.5103-0.35670.00840.3255-0.00060.15140.2378-0.05290.2641-26.67060.075355.5508
300.6091-0.4428-0.62271.25261.12562.10950.118-0.0140.08280.1371-0.0366-0.0835-0.0175-0.0357-0.03190.1073-0.01390.01490.0855-0.0050.1147-16.8375-15.649543.1737
310.87290.35170.00091.30580.54810.9840.1414-0.06080.10940.1796-0.0968-0.0265-0.1451-0.0101-0.03040.1852-0.02690.04510.1065-0.01330.1096-16.5417-9.780849.973
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 12 )A1 - 12
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 34 )A13 - 34
3X-RAY DIFFRACTION3chain 'A' and (resid 35 through 42 )A35 - 42
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 56 )A43 - 56
5X-RAY DIFFRACTION5chain 'A' and (resid 57 through 69 )A57 - 69
6X-RAY DIFFRACTION6chain 'A' and (resid 70 through 104 )A70 - 104
7X-RAY DIFFRACTION7chain 'A' and (resid 105 through 114 )A105 - 114
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 12 )B1 - 12
9X-RAY DIFFRACTION9chain 'B' and (resid 13 through 25 )B13 - 25
10X-RAY DIFFRACTION10chain 'B' and (resid 26 through 42 )B26 - 42
11X-RAY DIFFRACTION11chain 'B' and (resid 43 through 47 )B43 - 47
12X-RAY DIFFRACTION12chain 'B' and (resid 48 through 61 )B48 - 61
13X-RAY DIFFRACTION13chain 'B' and (resid 62 through 69 )B62 - 69
14X-RAY DIFFRACTION14chain 'B' and (resid 70 through 74 )B70 - 74
15X-RAY DIFFRACTION15chain 'B' and (resid 75 through 104 )B75 - 104
16X-RAY DIFFRACTION16chain 'B' and (resid 105 through 114 )B105 - 114
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 12 )C1 - 12
18X-RAY DIFFRACTION18chain 'C' and (resid 13 through 47 )C13 - 47
19X-RAY DIFFRACTION19chain 'C' and (resid 48 through 61 )C48 - 61
20X-RAY DIFFRACTION20chain 'C' and (resid 62 through 69 )C62 - 69
21X-RAY DIFFRACTION21chain 'C' and (resid 70 through 74 )C70 - 74
22X-RAY DIFFRACTION22chain 'C' and (resid 75 through 104 )C75 - 104
23X-RAY DIFFRACTION23chain 'C' and (resid 105 through 114 )C105 - 114
24X-RAY DIFFRACTION24chain 'D' and (resid 1 through 12 )D1 - 12
25X-RAY DIFFRACTION25chain 'D' and (resid 13 through 42 )D13 - 42
26X-RAY DIFFRACTION26chain 'D' and (resid 43 through 47 )D43 - 47
27X-RAY DIFFRACTION27chain 'D' and (resid 48 through 61 )D48 - 61
28X-RAY DIFFRACTION28chain 'D' and (resid 62 through 69 )D62 - 69
29X-RAY DIFFRACTION29chain 'D' and (resid 70 through 74 )D70 - 74
30X-RAY DIFFRACTION30chain 'D' and (resid 75 through 95 )D75 - 95
31X-RAY DIFFRACTION31chain 'D' and (resid 96 through 114 )D96 - 114

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