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- PDB-6s5p: Cfucosylated peptide SBL2 bound to Fucose binding Lectin LecB (PA... -

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Basic information

Entry
Database: PDB / ID: 6s5p
TitleCfucosylated peptide SBL2 bound to Fucose binding Lectin LecB (PA-IIL) from Pseudomonas aeruginosa at 1.46 Angstrom resolution
Components
  • Fucose-binding lectin
  • SBL2
KeywordsSUGAR BINDING PROTEIN / Lectin / Fucosylated
Function / homology
Function and homology information


single-species biofilm formation / carbohydrate binding / metal ion binding
Similarity search - Function
Lectin, sugar-binding / Calcium-mediated lectin / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-ZDC / 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: 1.46 Å
AuthorsBaeriswyl, S. / Stocker, A. / Reymond, J.-L.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
Citation
Journal: 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.
#1: Journal: Helv.Chim.Acta / Year: 2019
Title: X-Ray Crystal Structure of a Second Generation Peptide Dendrimer in Complex with Pseudomonas aeruginosa Lectin LecB
Authors: Baeriswyl, S. / Javor, S. / Stocker, A. / Darbre, T. / Reymond, J.-L.
History
DepositionJul 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
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
B: Fucose-binding lectin
C: Fucose-binding lectin
D: Fucose-binding lectin
H: SBL2
E: SBL2
F: SBL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,38119
Polymers49,2367
Non-polymers1,14512
Water7,404411
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-96 kcal/mol
Surface area16300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.099, 56.264, 70.498
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11D-454-

HOH

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Components

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


Mass: 11865.905 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Fucose binding lectin LecB (PA-LII) from Pseudomonas aeruginosa
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: lecB, C0044_25260, CAZ10_21840, DT376_00595, DY979_15445, ECC04_10105, EFK27_13700, EGV95_09240, EGY23_15550, IPC669_23070, PA5486_01888, 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: Protein/peptide SBL2


Mass: 590.759 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: SBL2 N-terminally fucosylated peptide linker / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#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 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Ammonium phosphate monobasic, 0.1 M Tris pH 8.5, 50% v/v (+/-)-2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000033 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 5, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000033 Å / Relative weight: 1
ReflectionResolution: 1.46→46.365 Å / Num. obs: 164044 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 23.4 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.168 / Net I/σ(I): 9.95
Reflection shellResolution: 1.46→1.467 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.04 / Num. unique obs: 26246 / CC1/2: 0.529 / Rrim(I) all: 1.801 / % possible all: 98.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.63 Å46.37 Å
Translation2.63 Å46.37 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.8.1phasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OXC

1oxc


Resolution: 1.46→46.365 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.25 / Phase error: 23.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1944 8222 5.02 %
Rwork0.1766 155666 -
obs0.1775 163888 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.29 Å2 / Biso mean: 23.7699 Å2 / Biso min: 12.86 Å2
Refinement stepCycle: final / Resolution: 1.46→46.365 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3340 0 118 411 3869
Biso mean--30.36 33.94 -
Num. residues----464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143435
X-RAY DIFFRACTIONf_angle_d0.9144703
X-RAY DIFFRACTIONf_chiral_restr0.093600
X-RAY DIFFRACTIONf_plane_restr0.004622
X-RAY DIFFRACTIONf_dihedral_angle_d18.7141131
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 (%)
1.4599-1.47650.41842580.40784946520494
1.4765-1.49390.38892710.391451505421100
1.4939-1.51210.38072790.36852075486100
1.5121-1.53120.36522740.338252205494100
1.5312-1.55140.31672740.311651745448100
1.5514-1.57260.31282800.308952155495100
1.5726-1.59510.31352720.282651645436100
1.5951-1.61890.2862740.282752125486100
1.6189-1.64420.27962720.271952075479100
1.6442-1.67120.27712790.268252185497100
1.6712-1.70.2772690.251751595428100
1.7-1.73090.27362780.237752155493100
1.7309-1.76420.24962760.226952165492100
1.7642-1.80020.23882800.21751755455100
1.8002-1.83940.22112750.206752045479100
1.8394-1.88220.22472710.197652025473100
1.8822-1.92920.18342780.176851925470100
1.9292-1.98140.21212760.163951735449100
1.9814-2.03970.15892720.162151805452100
2.0397-2.10550.19332720.164552315503100
2.1055-2.18080.1962730.165251945467100
2.1808-2.26810.16552680.145651955463100
2.2681-2.37130.16232800.142252095489100
2.3713-2.49630.14222790.137451715450100
2.4963-2.65270.14642760.136452135489100
2.6527-2.85750.13982730.130651845457100
2.8575-3.1450.17612760.129952205496100
3.145-3.60.14662740.126952005474100
3.6-4.5350.1672670.138152115478100
4.535-46.38850.18552760.1952095485100
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)
10.29510.15660.01550.9888-0.40440.89090.01180.01270.0214-0.1412-0.0187-0.00040.0952-0.0250.00690.27740.00440.00230.1576-0.00530.1628-29.74658.6715-29.4385
20.27180.3031-0.42081.7582-0.97191.0121-0.01470.07260.0242-0.2460.0204-0.00030.0975-0.0622-0.00520.3116-0.0114-0.01660.1697-0.00760.157-28.588111.3541-33.4898
35.28711.43215.38433.062.6085.96850.2942-0.2216-0.364-0.0557-0.20130.66750.3613-0.39370.09110.277-0.0037-0.02260.1821-0.01170.2166-42.53374.4824-24.528
40.40720.36980.09390.56820.08460.210.0268-0.01850.0806-0.0098-0.01060.0374-0.0107-0.0127-0.01360.2710.00220.0020.154800.1671-26.169812.9555-22.1128
54.59774.7264-2.14156.1364-2.26871.65830.0807-0.1579-0.02080.0759-0.1158-0.1462-0.00340.02510.02930.25720.00990.00120.1543-0.00480.1867-13.97739.2809-8.605
60.9107-0.1478-0.91471.2479-0.48175.6681-0.03490.0316-0.1198-0.0383-0.0096-0.14730.31060.23950.06770.25170.01850.00590.1131-0.01380.1968-10.25952.9154-22.4981
70.98180.5432-2.99461.4649-0.69289.9027-0.1495-0.1271-0.1727-0.1155-0.0852-0.14720.78040.28810.24230.28880.01880.01050.15050.00160.2057-16.113-1.4099-19.3207
84.55341.3708-4.5890.6134-0.62177.20080.0196-0.4333-0.11350.1085-0.1098-0.15640.00040.45010.07950.30840.0244-0.01080.19260.01460.2124-9.55355.1647-10.7866
95.354-5.4532-1.51146.31493.04843.39050.31590.59750.3503-0.7311-0.055-1.21480.35210.6243-0.32620.3330.05860.09410.2581-0.02410.3411.79337.88-24.9315
101.1848-0.7889-0.52040.97870.63930.74430.0331-0.00460.0358-0.0555-0.0082-0.1072-0.02530.0441-0.01360.24630.00680.01120.1494-0.00370.1785-14.306714.4894-20.4189
112.71811.233-2.56290.716-1.28622.505-0.07180.00480.0449-0.19670.08270.02880.16740.00360.01110.24890.00610.01070.1373-0.00450.1638-20.38985.9932-16.8724
123.82430.8143.92340.33011.31075.98660.0071-0.0533-0.176-0.01930.0371-0.03560.0082-0.0521-0.04770.26850.0050.02090.14060.00140.169-28.864219.1377-3.418
132.4513-2.14291.42133.5521-2.6922.1609-0.0493-0.04270.19870.0989-0.0691-0.0996-0.1823-0.06450.19570.29850.01440.02340.1325-0.0230.1713-29.88234.7097-7.749
140.03770.3594-0.40762.2009-2.55943.26180.0103-0.0229-0.00270.25790.0640.278-0.1766-0.1107-0.14470.3020.02320.01810.16640.0040.2048-35.597530.4785-0.9693
153.8169-2.5157-0.27672.49471.01281.9569-0.01070.16360.4308-0.17990.0518-0.069-0.38980.0228-0.12160.32950.00470.00680.14790.00550.2083-31.508142.5485-14.7715
161.3991-2.55573.50884.7169-6.37178.679-0.0136-0.0741-0.00990.50240.08070.3012-0.53-0.0038-0.06010.29610.01420.01630.1571-0.01460.1711-26.889433.962-0.5581
173.3967-2.54775.08323.7637-4.71858.06260.0516-0.2327-0.0973-0.00730.1320.19180.0823-0.3084-0.32860.2710.0170.03270.17290.00650.1882-33.351523.1268-1.1436
184.23254.18661.6824.3191.35751.80430.14760.06170.65480.6365-0.09511.4347-0.4896-0.5164-0.06460.32780.03860.07210.1894-0.00070.3416-44.736832.718-10.7063
191.8147-0.83720.02691.0492-0.04990.1468-0.0818-0.007-0.01370.0550.05740.0494-0.10090.0050.03130.24190.00630.01170.14370.00080.1621-24.69722.9797-11.3675
201.3896-0.7795-0.43231.9516-0.08880.99490.08280.1547-0.2301-0.2535-0.06740.1379-0.0373-0.10320.00840.25170.0283-0.02920.1801-0.0090.2019-37.803632.3464-20.5585
212.4966-1.28081.21960.7485-0.86991.26880.0612-0.07640.01490.00510.02250.0853-0.0260.0483-0.07220.26010.00760.01390.1466-0.00020.1702-22.699827.8603-5.3526
225.7314-3.92152.96115.4276-2.57182.49650.09050.15990.0291-0.2892-0.0682-0.09670.18820.0266-0.02990.2714-0.00970.01710.15330.00720.1538-15.118331.3104-24.8667
231.30830.22561.72770.8603-0.22937.02120.01220.00390.1568-0.0935-0.01160.028-0.14380.23770.02530.2814-0.00410.02240.1079-0.01440.1972-13.140837.8833-13.3867
243.0288-2.04910.57352.25060.94832.17080.00040.18820.1136-0.2834-0.0689-0.039-1.15670.06670.02280.3316-0.0437-0.00440.13620.00090.2213-10.764943.2245-15.7852
259.14771.64566.04166.3121.55154.04430.1102-0.37310.15920.52470.05390.185-0.0868-0.1279-0.14070.2853-0.0240.04940.1987-0.02930.1775-15.018436.0860.8572
262.299-0.62372.63211.2483-0.23.6402-0.10720.02070.208-0.1043-0.0038-0.0294-0.79020.21710.30030.3085-0.00550.01010.1206-0.00730.2067-19.180342.0425-14.7919
274.8075-0.93154.790.1943-0.8616.4162-0.07580.32440.2835-0.1544-0.1333-0.11270.12160.32630.32280.2976-0.02290.02660.1670.0310.1994-11.396136.0567-22.6647
288.68825.91483.14495.13244.57756.54440.3462-0.0946-0.22250.8264-0.0578-0.36250.327-0.0047-0.25090.2659-0.0019-0.01770.13230.01010.2145-0.533834.8993-8.0242
290.340.1649-0.03070.11630.05180.27180.0151-0.0290.0291-0.045-0.0041-0.0061-0.0676-0.0059-0.00050.24480.0010.00690.1405-0.00150.1731-17.147228.4182-13.9995
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 48 )A1 - 48
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 68 )A49 - 68
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 74 )A69 - 74
4X-RAY DIFFRACTION4chain 'A' and (resid 75 through 114 )A75 - 114
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 12 )B1 - 12
6X-RAY DIFFRACTION6chain 'B' and (resid 13 through 48 )B13 - 48
7X-RAY DIFFRACTION7chain 'B' and (resid 49 through 56 )B49 - 56
8X-RAY DIFFRACTION8chain 'B' and (resid 57 through 68 )B57 - 68
9X-RAY DIFFRACTION9chain 'B' and (resid 69 through 74 )B69 - 74
10X-RAY DIFFRACTION10chain 'B' and (resid 75 through 104 )B75 - 104
11X-RAY DIFFRACTION11chain 'B' and (resid 105 through 114 )B105 - 114
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 12 )C1 - 12
13X-RAY DIFFRACTION13chain 'C' and (resid 13 through 25 )C13 - 25
14X-RAY DIFFRACTION14chain 'C' and (resid 26 through 42 )C26 - 42
15X-RAY DIFFRACTION15chain 'C' and (resid 43 through 48 )C43 - 48
16X-RAY DIFFRACTION16chain 'C' and (resid 49 through 56 )C49 - 56
17X-RAY DIFFRACTION17chain 'C' and (resid 57 through 68 )C57 - 68
18X-RAY DIFFRACTION18chain 'C' and (resid 69 through 74 )C69 - 74
19X-RAY DIFFRACTION19chain 'C' and (resid 75 through 95 )C75 - 95
20X-RAY DIFFRACTION20chain 'C' and (resid 96 through 104 )C96 - 104
21X-RAY DIFFRACTION21chain 'C' and (resid 105 through 114 )C105 - 114
22X-RAY DIFFRACTION22chain 'D' and (resid 1 through 12 )D1 - 12
23X-RAY DIFFRACTION23chain 'D' and (resid 13 through 34 )D13 - 34
24X-RAY DIFFRACTION24chain 'D' and (resid 35 through 42 )D35 - 42
25X-RAY DIFFRACTION25chain 'D' and (resid 43 through 48 )D43 - 48
26X-RAY DIFFRACTION26chain 'D' and (resid 49 through 56 )D49 - 56
27X-RAY DIFFRACTION27chain 'D' and (resid 57 through 68 )D57 - 68
28X-RAY DIFFRACTION28chain 'D' and (resid 69 through 74 )D69 - 74
29X-RAY DIFFRACTION29chain 'D' and (resid 75 through 114 )D75 - 114

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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