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- PDB-6s5r: Cfucosylated second generation peptide dendrimer SBD6 bound to Fu... -

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Basic information

Entry
Database: PDB / ID: 6s5r
TitleCfucosylated second generation peptide dendrimer SBD6 bound to Fucose binding Lectin LecB (PA-IIL) from Pseudomonas aeruginosa at 2.08 Angstrom resolution, incomplete structure
Components
  • Fucose-binding lectin
  • SBD6
KeywordsSUGAR BINDING PROTEIN / Lectin / Fucosylated / Dendrimer / Second Generation
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 / polypeptide(D) / 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: 2.076 Å
AuthorsBaeriswyl, S. / Stocker, A. / Reymond, J.-L.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: 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 1.1Jul 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 1.2Jan 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
F: SBD6
H: SBD6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,40018
Polymers48,2556
Non-polymers1,14512
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-116 kcal/mol
Surface area17370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.003, 91.003, 315.583
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-456-

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-IIL) 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: Polypeptide(D) SBD6


Mass: 395.455 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Cfucosylated second generation peptide dendrimer SBD6, incomplete first generation
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


Mass: 18.015 Da / Num. of mol.: 244 / 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: 3.97 Å3/Da / Density % sol: 69.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M Potassium sodium tartrate tetrahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 2.0 M Ammonium sulfate

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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: Sep 23, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000033 Å / Relative weight: 1
ReflectionResolution: 2.076→45.036 Å / Num. obs: 88116 / % possible obs: 99.6 % / Redundancy: 5.2 % / Biso Wilson estimate: 43.5 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.2 / Net I/σ(I): 7.17
Reflection shellResolution: 2.076→2.086 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 0.76 / Num. unique obs: 13946 / CC1/2: 0.217 / Rrim(I) all: 2.08 / % possible all: 98.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.08 Å45.04 Å
Translation2.08 Å45.04 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.7.16phasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OXC

1oxc


Resolution: 2.076→45.036 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.28 / Phase error: 24.23
RfactorNum. reflection% reflection
Rfree0.237 4386 4.98 %
Rwork0.2051 --
obs0.2067 87991 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.72 Å2 / Biso mean: 51.5955 Å2 / Biso min: 24.18 Å2
Refinement stepCycle: final / Resolution: 2.076→45.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3326 0 93 244 3663
Biso mean--72.18 54.49 -
Num. residues----456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133412
X-RAY DIFFRACTIONf_angle_d1.1614676
X-RAY DIFFRACTIONf_chiral_restr0.06596
X-RAY DIFFRACTIONf_plane_restr0.007618
X-RAY DIFFRACTIONf_dihedral_angle_d3.5471948
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 (%)
2.0757-2.09930.34621320.3262576270894
2.0993-2.1240.36251370.32852811294899
2.124-2.14990.3461390.32272727286699
2.1499-2.17710.32071490.322728062955100
2.1771-2.20580.34121500.311228082958100
2.2058-2.2360.32761490.302227682917100
2.236-2.26790.31631480.297828222970100
2.2679-2.30180.2991510.279527532904100
2.3018-2.33780.28081480.290728523000100
2.3378-2.37610.3331410.289227622903100
2.3761-2.41710.30141500.283328072957100
2.4171-2.4610.33131410.267928623003100
2.461-2.50830.29261440.264727522896100
2.5083-2.55950.33231460.256428052951100
2.5595-2.61520.29051460.246527882934100
2.6152-2.6760.2551500.225528312981100
2.676-2.74290.26711490.216427632912100
2.7429-2.81710.2231520.223627952947100
2.8171-2.90.33061450.225828042949100
2.9-2.99350.23341460.216127582904100
2.9935-3.10050.22991460.20682771291799
3.1005-3.22460.22121440.201228102954100
3.2246-3.37130.22161520.183328222974100
3.3713-3.5490.22491410.161327592900100
3.549-3.77130.22751490.152428162965100
3.7713-4.06230.1921450.173527932938100
4.0623-4.47070.19361510.15327982949100
4.4707-5.11690.15711490.139628002949100
5.1169-6.44370.18931450.184227852930100
6.4437-45.04640.21741510.207528012952100
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)
13.1147-2.05281.94135.22540.50042.87530.3469-0.0676-0.5879-0.3706-0.15220.22510.30910.3203-0.29770.45780.0445-0.14690.2234-0.00540.4984-32.338314.625119.9444
22.3468-2.7392.14246.7534-4.35453.26180.6570.0347-0.6356-1.88690.93841.83890.7651-0.9719-1.46670.9114-0.0156-0.40220.43560.01570.7829-40.398715.374912.4106
33.404-1.52042.30242.6255-0.27463.33780.43840.1516-0.8294-1.10520.08210.79480.6874-0.1383-0.57940.74260.0809-0.20660.2978-0.01630.6262-32.123312.150917.0059
42.7103-0.46930.10647.1345-7.18037.17570.10620.3373-0.5019-1.69270.18710.91830.9761-0.7357-0.37411.0360.0062-0.40580.4238-0.05410.7982-41.102219.973812.2343
51.77610.0377-2.46460.81941.94738.26460.2011-0.0161-2.2043-0.57280.90591.46281.5922-0.1805-0.69180.6456-0.0219-0.40910.61010.1871.6433-46.57048.456722.1506
62.7333-2.64620.61754.4330.33870.6260.164-0.0915-0.4664-0.51530.07150.55490.1047-0.2211-0.23920.42660.0314-0.10880.28690.05910.3931-35.349123.333922.633
73.6795-1.7956-0.65655.4944-0.73724.2252-0.0719-0.3410.0786-0.16530.2256-0.56880.4960.565-0.12840.38530.10340.01880.3034-0.00590.3928-18.517323.221427.5466
83.5779-1.0566-0.75854.6844-0.55944.42460.0764-0.39940.2338-0.04780.091-0.57940.25860.2304-0.18930.33590.1175-0.04120.3327-0.05090.3868-18.651521.92231.0259
98.1071-7.6925-6.88468.01066.59935.85520.5970.3409-0.2151-1.22680.1063-1.59350.50261.4873-0.38270.6830.1470.1270.6679-0.05891.0076-7.617631.075820.9422
102.7586-2.6840.40893.67950.81631.14640.03-0.1856-0.063-0.29420.0271-0.2674-0.0751-0.0411-0.10640.38720.0636-0.03640.2707-0.00320.3039-26.042827.913225.1189
113.4577-0.52481.43313.25371.25442.8744-0.027-0.2586-0.22710.84580.05670.25990.0358-0.10660.03380.56520.00490.08160.21240.01050.2869-9.40015.573212.6628
129.05744.50544.06365.5813.15532.8327-0.2022-0.4740.35120.82920.02080.37890.159-0.16160.17960.80340.06160.16040.3523-0.0210.3659-12.263610.801418.7004
133.57883.95652.75919.55766.68014.6766-0.1042-0.5255-0.91961.5984-0.0278-0.82721.11931.0497-0.25641.1640.029-0.28040.42430.04280.33456.21496.695522.3019
146.94352.3993.03134.13491.77532.9708-0.2593-0.73760.1640.8016-0.03650.67870.1376-0.36460.23730.71530.05960.17330.27480.00790.2929-13.04026.23715.591
158.9097-5.4098-3.59683.45472.93935.05930.2697-1.25811.21060.3526-0.6259-1.1812-0.211-0.8350.34760.695-0.00610.01370.5113-0.07780.4417-2.495921.112418.3426
160.7084-0.10660.53972.53460.93052.66290.0361-0.07570.02420.41550.0076-0.07210.036-0.0006-0.06920.41920.01640.02510.18160.00560.2513-4.13234.2848.823
171.15611.5052-0.12134.21673.72197.37960.07530.04780.03390.34740.4632-1.14750.38170.606-0.50950.39720.0831-0.12690.2235-0.04590.6169.5093-7.52585.1683
186.71021.3487-0.61723.90520.42922.4791-0.0242-0.543-0.23551.97730.303-0.54780.43460.41930.08191.26850.1469-0.11630.23730.11550.3620.6879-11.797617.0252
192.33420.0436-0.80133.89871.2372.99010.134-0.5679-0.33441.6510.262-1.3541.23250.3275-0.05350.8840.1697-0.31360.3064-0.02520.54017.248-9.415614.1248
200.619-0.52710.08322.95560.50140.66670.0019-0.1213-0.13160.69690.1661-0.10310.24710.0433-0.1140.580.0033-0.03780.23360.0340.3046-1.7347-7.89188.4212
214.706-1.58320.20953.04011.26040.82950.24060.38030.0332-1.3938-0.02950.9755-0.1341-0.3948-0.18730.80.0568-0.1530.31570.03460.4588-39.68627.132712.8267
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 13 through 25 )C13 - 25
2X-RAY DIFFRACTION2chain 'C' and (resid 26 through 34 )C26 - 34
3X-RAY DIFFRACTION3chain 'C' and (resid 35 through 56 )C35 - 56
4X-RAY DIFFRACTION4chain 'C' and (resid 57 through 69 )C57 - 69
5X-RAY DIFFRACTION5chain 'C' and (resid 70 through 74 )C70 - 74
6X-RAY DIFFRACTION6chain 'C' and (resid 75 through 114 )C75 - 114
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 47 )D1 - 47
8X-RAY DIFFRACTION8chain 'D' and (resid 48 through 69 )D48 - 69
9X-RAY DIFFRACTION9chain 'D' and (resid 70 through 74 )D70 - 74
10X-RAY DIFFRACTION10chain 'D' and (resid 75 through 114 )D75 - 114
11X-RAY DIFFRACTION11chain 'A' and (resid 1 through 25 )A1 - 25
12X-RAY DIFFRACTION12chain 'A' and (resid 26 through 42 )A26 - 42
13X-RAY DIFFRACTION13chain 'A' and (resid 43 through 47 )A43 - 47
14X-RAY DIFFRACTION14chain 'A' and (resid 48 through 68 )A48 - 68
15X-RAY DIFFRACTION15chain 'A' and (resid 69 through 74 )A69 - 74
16X-RAY DIFFRACTION16chain 'A' and (resid 75 through 114 )A75 - 114
17X-RAY DIFFRACTION17chain 'B' and (resid 1 through 12 )B1 - 12
18X-RAY DIFFRACTION18chain 'B' and (resid 13 through 47 )B13 - 47
19X-RAY DIFFRACTION19chain 'B' and (resid 48 through 68 )B48 - 68
20X-RAY DIFFRACTION20chain 'B' and (resid 69 through 114 )B69 - 114
21X-RAY DIFFRACTION21chain 'C' and (resid 1 through 12 )C1 - 12

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