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- PDB-5d2a: Bifunctional dendrimers -

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Basic information

Entry
Database: PDB / ID: 5d2a
TitleBifunctional dendrimers
Components
  • (ZDC-ALA-PRO-ALA-LYS-PHE-CYS-ALA-PRO-ALA-PHB- ...) x 2
  • Fucose-binding lectin
KeywordsSUGAR BINDING PROTEIN / LectinB / Pseudomonas / Dendrimer / Biofilm / Bifunctional
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
beta-D-galactopyranose / P-HYDROXYBENZOIC ACID / 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: 2.134 Å
AuthorsMichaud, G. / Visini, R. / Stocker, A. / Darbre, T. / Reymond, J.L.
CitationJournal: Chem Sci / Year: 2016
Title: Overcoming antibiotic resistance inPseudomonas aeruginosabiofilms using glycopeptide dendrimers.
Authors: Michaud, G. / Visini, R. / Bergmann, M. / Salerno, G. / Bosco, R. / Gillon, E. / Richichi, B. / Nativi, C. / Imberty, A. / Stocker, A. / Darbre, T. / Reymond, J.L.
History
DepositionAug 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 8, 2019Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: ZDC-ALA-PRO-ALA-LYS-PHE-CYS-ALA-PRO-ALA-PHB-GAL
D: ZDC-ALA-PRO-ALA-LYS-PHE-CYS-ALA-PRO-ALA-PHB-GAL
E: ZDC-ALA-PRO-ALA-LYS-PHE-CYS-ALA-PRO-ALA-PHB-GAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,51213
Polymers24,6215
Non-polymers8918
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-67 kcal/mol
Surface area10090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.107, 105.107, 111.092
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Fucose-binding lectin / Fucose-binding lectin PA-IIL / Photopexin A / Pseudomonas aeruginosa genome assembly PAE221


Mass: 11734.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: lecB, ERS445055_01627, PA8380_17510, PAE221_03716, PAMH19_1713, YQ19_10010
Production host: Escherichia coli (E. coli) / References: UniProt: A0A069Q9V4, UniProt: Q9HYN5*PLUS

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ZDC-ALA-PRO-ALA-LYS-PHE-CYS-ALA-PRO-ALA-PHB- ... , 2 types, 3 molecules CDE

#2: Protein/peptide ZDC-ALA-PRO-ALA-LYS-PHE-CYS-ALA-PRO-ALA-PHB-GAL


Mass: 636.782 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide ZDC-ALA-PRO-ALA-LYS-PHE-CYS-ALA-PRO-ALA-PHB-GAL


Mass: 257.286 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Sugars , 2 types, 3 molecules

#6: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose / Galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: 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.: 2 / Source method: obtained synthetically / Formula: C8H14O6

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Non-polymers , 3 types, 84 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PHB / P-HYDROXYBENZOIC ACID / 4-Hydroxybenzoic acid


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 3.77 Å3/Da / Density % sol: 67.41 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 2M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.13→47.506 Å / Num. obs: 38033 / % possible obs: 99.5 % / Redundancy: 10.28 % / Rsym value: 0.13 / Net I/σ(I): 14.95

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CE8

4ce8


Resolution: 2.134→47.506 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1995 9.68 %Random selection
Rwork0.205 18612 --
obs0.2091 20607 99.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.67 Å2 / Biso mean: 53.1255 Å2 / Biso min: 40.12 Å2
Refinement stepCycle: final / Resolution: 2.134→47.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1634 0 127 79 1840
Biso mean--86.07 52.04 -
Num. residues----228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011784
X-RAY DIFFRACTIONf_angle_d1.322453
X-RAY DIFFRACTIONf_chiral_restr0.051313
X-RAY DIFFRACTIONf_plane_restr0.005321
X-RAY DIFFRACTIONf_dihedral_angle_d14.594566
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1342-2.18760.40591320.35811236136894
2.1876-2.24670.35011380.322812971435100
2.2467-2.31290.35381400.293812971437100
2.3129-2.38750.31591410.27541301144299
2.3875-2.47280.2991400.261413091449100
2.4728-2.57180.33891400.250513091449100
2.5718-2.68890.31571420.232413221464100
2.6889-2.83060.26871420.229813211463100
2.8306-3.00790.27951410.225913261467100
3.0079-3.24010.29721420.225913271469100
3.2401-3.56610.23561440.184313471491100
3.5661-4.08190.21061450.170613481493100
4.0819-5.14180.16151490.142213821531100
5.1418-47.51770.2151590.176514901649100

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