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- PDB-4ce8: Perdeuterated Pseudomonas aeruginosa Lectin II complex with hydro... -

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Basic information

Entry
Database: PDB / ID: 4ce8
TitlePerdeuterated Pseudomonas aeruginosa Lectin II complex with hydrogenated L-Fucose and Calcium
ComponentsFUCOSE-BINDING LECTIN PA-IIL
KeywordsSUGAR BINDING PROTEIN / PERDEUTERATED
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
alpha-L-fucopyranose / UREA / Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å
AuthorsCuypers, M.G. / Mitchell, E.P. / Mossou, E. / Pokorna, M. / Wimmerova, M. / Imberty, A. / Moulin, M. / Haertlein, M. / Forsyth, V.T.
CitationJournal: To be Published
Title: Perdeuterated Pseudomonas Aeruginosa Lectin II Complex with Hydrogenated L Fucose and Calcium
Authors: Cuypers, M.G. / Mossou, E. / Mitchell, E.P. / Russi, S. / Pokorna, M. / Wimmerova, M. / Imberty, A. / Mcsweeney, S. / Haertlein, M. / Forsyth, V.T.
History
DepositionNov 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / chem_comp / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_alt_id / _atom_site.label_atom_id / _atom_site.occupancy / _chem_comp.type / _pdbx_database_status.status_code_sf
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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 / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_dist_value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Dec 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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 PA-IIL
B: FUCOSE-BINDING LECTIN PA-IIL
C: FUCOSE-BINDING LECTIN PA-IIL
D: FUCOSE-BINDING LECTIN PA-IIL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,84126
Polymers46,9394
Non-polymers1,90222
Water17,817989
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12180 Å2
ΔGint-191.3 kcal/mol
Surface area15460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.480, 72.490, 54.610
Angle α, β, γ (deg.)90.00, 94.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
FUCOSE-BINDING LECTIN PA-IIL


Mass: 11734.707 Da / Num. of mol.: 4 / Fragment: 2-115
Source method: isolated from a genetically manipulated source
Details: PERDEUTERATED PROTEIN / Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HYN5
#3: Sugar
ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 1007 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4N2O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 989 / 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: 2.21 Å3/Da / Density % sol: 44.28 %
Description: NEEDED ONLY 2 CA ATOMS FROM 1UZV FOR ISOMORPHOUS REPLACEMENT WITH ACORN.
Crystal growMethod: vapor diffusion, hanging drop
Details: ALL SALTS EXCHANGED 3X AGAINST D2O. 0,1 M TRIS PD 8.5, 1.75M (ND4)2SO4, 2MM CACL2, 2MM MGCL2. 10 MG/ML PROTEIN PRE-INCUBATED IN 2MM CACL2 AND 250 MG/L L-FUCOSE. HANGING DROP METHOD.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8266
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 0.9→43.55 Å / Num. obs: 291511 / % possible obs: 97.1 % / Observed criterion σ(I): 1.8 / Redundancy: 3 % / Biso Wilson estimate: 6.16 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.2
Reflection shellHighest resolution: 0.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.8 / % possible all: 94.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
ACORNphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UZV

1uzv


Resolution: 0.9→36.463 Å / SU ML: 0.07 / σ(F): 1.34 / Phase error: 13.29 / Stereochemistry target values: ML
Details: UREA FOUND NEARBY ARGININES, PARTIAL DEGRADATION POSSIBLE INTO ORNITHINE.
RfactorNum. reflection% reflection
Rfree0.1405 24069 5 %
Rwork0.1247 --
obs0.1255 291449 80.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 4.23 Å2
Refinement stepCycle: LAST / Resolution: 0.9→36.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 101 989 4398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153764
X-RAY DIFFRACTIONf_angle_d1.3595151
X-RAY DIFFRACTIONf_dihedral_angle_d12.771288
X-RAY DIFFRACTIONf_chiral_restr0.082643
X-RAY DIFFRACTIONf_plane_restr0.007692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9-0.91020.32936940.29513948X-RAY DIFFRACTION73
0.9102-0.92090.29427570.276913841X-RAY DIFFRACTION74
0.9209-0.93220.27747630.257113980X-RAY DIFFRACTION74
0.9322-0.9440.24357180.240514189X-RAY DIFFRACTION75
0.944-0.95640.22557270.228414104X-RAY DIFFRACTION75
0.9564-0.96950.22057130.211514315X-RAY DIFFRACTION76
0.9695-0.98330.21327660.210114165X-RAY DIFFRACTION76
0.9833-0.9980.20238510.194214375X-RAY DIFFRACTION76
0.998-1.01360.19647790.175214427X-RAY DIFFRACTION77
1.0136-1.03020.18757380.16214615X-RAY DIFFRACTION77
1.0302-1.0480.1627130.149414601X-RAY DIFFRACTION78
1.048-1.06710.14577980.134114745X-RAY DIFFRACTION78
1.0671-1.08760.13128480.117114658X-RAY DIFFRACTION78
1.0876-1.10980.11947990.107714850X-RAY DIFFRACTION79
1.1098-1.13390.11887140.100315087X-RAY DIFFRACTION79
1.1339-1.16030.11358400.095714938X-RAY DIFFRACTION80
1.1603-1.18930.10748880.096314983X-RAY DIFFRACTION80
1.1893-1.22150.10968640.095715113X-RAY DIFFRACTION81
1.2215-1.25740.1128380.09415288X-RAY DIFFRACTION81
1.2574-1.2980.11518160.094915364X-RAY DIFFRACTION82
1.298-1.34440.117910.091715409X-RAY DIFFRACTION82
1.3444-1.39820.10648240.096115637X-RAY DIFFRACTION83
1.3982-1.46190.11698410.09915660X-RAY DIFFRACTION83
1.4619-1.53890.11528370.097315659X-RAY DIFFRACTION83
1.5389-1.63540.1198290.098515693X-RAY DIFFRACTION83
1.6354-1.76160.14098870.113116399X-RAY DIFFRACTION87
1.7616-1.93890.11858780.110516771X-RAY DIFFRACTION89
1.9389-2.21940.11538810.105816983X-RAY DIFFRACTION90
2.2194-2.79610.1438140.125317232X-RAY DIFFRACTION91
2.7961-36.49270.1488630.128217042X-RAY DIFFRACTION90

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