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- PDB-4cp9: Crystal structure OF lecA lectin complexed with a divalent galact... -

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Basic information

Entry
Database: PDB / ID: 4cp9
TitleCrystal structure OF lecA lectin complexed with a divalent galactoside at 1.65 angstrom
Components(PA-I GALACTOPHILIC ...) x 2
KeywordsSUGAR BINDING PROTEIN / GALACTOSE BINDING / SUGAR BASED INHIBITOR
Function / homology
Function and homology information


heterophilic cell-cell adhesion / carbohydrate binding / periplasmic space / cell surface / cytoplasm
Similarity search - Function
PA-IL-like / PA-IL-like protein / Galactose-binding lectin / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-CN8 / beta-D-galactopyranose / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
Model type detailsCA ATOMS ONLY, CHAIN A, B, C, D
AuthorsTopin, J. / Varrot, A. / Imberty, A. / Wissinger, N.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: A Leca Ligand Identified from a Galactoside-Conjugate Array Inhibits Host Cell Invasion by Pseudomonas Aeruginosa.
Authors: Novoa, A. / Eierhoff, T. / Topin, J. / Varrot, A. / Barluenga, S. / Imberty, A. / Romer, W. / Winssinger, N.
History
DepositionFeb 4, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Derived calculations / Non-polymer description / Other
Revision 1.2Dec 28, 2016Group: Structure summary
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: 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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PA-I GALACTOPHILIC LECTIN
B: PA-I GALACTOPHILIC LECTIN
C: PA-I GALACTOPHILIC LECTIN
D: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,39324
Polymers51,2894
Non-polymers4,10520
Water7,530418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8776
Polymers12,8341
Non-polymers1,0435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8897
Polymers12,8181
Non-polymers1,0716
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7655
Polymers12,8181
Non-polymers9474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8616
Polymers12,8181
Non-polymers1,0435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.876, 66.259, 159.427
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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PA-I GALACTOPHILIC ... , 2 types, 4 molecules ABCD

#1: Protein PA-I GALACTOPHILIC LECTIN / PA-IL / GALACTOSE-BINDING LECTIN / LECA


Mass: 12834.134 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: OXIDATED CYS57 / Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05097
#2: Protein PA-I GALACTOPHILIC LECTIN / PA-IL / GALACTOSE-BINDING LECTIN / LECA


Mass: 12818.134 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: OXIDATED CYS57 / Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05097

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Sugars , 1 types, 4 molecules

#4: Sugar
ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
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

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Non-polymers , 6 types, 434 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-CN8 / (4S)-N-ethyl-4-{[N-methyl-3-(1-{2-[(4-sulfanylbenzoyl)amino]ethyl}-1H-1,2,3-triazol-4-yl)-L-alanyl]amino}-L-prolinamide


Mass: 488.606 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H32N8O3S
#6: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsN-TERMINAL METHIONINE CLEAVED

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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: 2.63 Å3/Da / Density % sol: 53.3 % / Description: NONE
Crystal growpH: 8.5
Details: SOLUTION 20 OF THE CSSI SCREEN 8% PEG 20K, 8% PEG550MME, 100 MM TRIS 8.5 AND 0.2 M LI2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESERACH / Detector: CCD / Date: Jul 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.65→48.47 Å / Num. obs: 65807 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 22.9
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OKO

1oko


Resolution: 1.65→48.47 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.38 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.18362 3334 5.1 %RANDOM
Rwork0.15525 ---
obs0.15665 62390 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.643 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å20 Å2
2--2.17 Å20 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 1.65→48.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3614 0 194 418 4226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193973
X-RAY DIFFRACTIONr_bond_other_d0.0020.023602
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.9775416
X-RAY DIFFRACTIONr_angle_other_deg0.78338275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0415498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63725.915164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.70715530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.514158
X-RAY DIFFRACTIONr_chiral_restr0.1050.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214639
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02919
X-RAY DIFFRACTIONr_nbd_refined0.2410.21061
X-RAY DIFFRACTIONr_nbd_other0.1810.23359
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21940
X-RAY DIFFRACTIONr_nbtor_other0.0810.21805
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2132
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1540.218
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.280.242
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1780.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2011.5931977
X-RAY DIFFRACTIONr_mcbond_other1.21.5931976
X-RAY DIFFRACTIONr_mcangle_it1.8092.3812480
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.172.0381996
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 251 -
Rwork0.22 4541 -
obs--99.98 %
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)
10.6458-0.10010.31440.2060.52793.1952-0.0140.0342-0.03630.02340.0566-0.01920.02740.2034-0.04260.01980.01870.00060.1250.01240.012138.78440.16216.426
20.8687-0.443-0.24350.98641.2992.3633-0.0552-0.0249-0.09440.0548-0.08070.04330.0163-0.1830.13590.01330.0108-0.00240.1402-0.01350.039217.33446.15216.334
31.9528-0.491-0.46431.10521.52352.12980.01450.3447-0.1806-0.0176-0.17360.1263-0.0342-0.20010.15910.0303-0.02440.00320.1862-0.0870.044313.18230.383-20.704
40.6053-0.11890.03040.16060.64593.1788-0.03640.0404-0.00930.05810.0090.01350.2490.1910.02740.08520.00790.01910.1269-0.03160.013435.30826.992-21.658
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 121
2X-RAY DIFFRACTION2B1 - 121
3X-RAY DIFFRACTION3C1 - 121
4X-RAY DIFFRACTION4D1 - 121

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