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- PDB-4cpb: CRYSTAL STRUCTURE OF LECA IN COMPLEX WITH A DIVALENT GALACTOSIDE ... -

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Basic information

Entry
Database: PDB / ID: 4cpb
TitleCRYSTAL STRUCTURE OF LECA IN COMPLEX WITH A DIVALENT GALACTOSIDE AT 1. 57 ANGSTROM IN MAGNESIUM
Components(PA-I GALACTOPHILIC ...) x 2
KeywordsSUGAR BINDING PROTEIN / GALACTOSE BINDING / SUGAR BASED INHIBITOR
Function / homology
Function and homology information


heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / 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 / DI(HYDROXYETHYL)ETHER / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
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 1.1Jul 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 1.2Dec 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.
Remark 700 SHEET 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)54,77420
Polymers51,3214
Non-polymers3,45316
Water6,521362
1


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


Theoretical massNumber of molelcules
Total (without water)27,25410
Polymers25,6682
Non-polymers1,5868
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-20.9 kcal/mol
Surface area10660 Å2
MethodPISA
3
C: PA-I GALACTOPHILIC LECTIN
D: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,52010
Polymers25,6522
Non-polymers1,8688
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-38.8 kcal/mol
Surface area11040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.666, 65.393, 159.869
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.: 3
Source method: isolated from a genetically manipulated source
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.: 1
Source method: isolated from a genetically manipulated source
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 / 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 , 7 types, 374 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-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#9: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.6 Å3/Da / Density % sol: 52.74 % / Description: THERE WAS A HIGH AND LOW RESOLUTION PASSES
Crystal growpH: 8.5
Details: SOLUTION 15 OF THE CSSI SCREEN 10 % PEG 8K, 10% PEG 1K, 100 MM TRIS 8.5 AND 200 MM MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.004
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.004 Å / Relative weight: 1
ReflectionResolution: 1.57→39.97 Å / Num. obs: 75110 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.2
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 4 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.9 / % possible all: 99.4

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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: 1.57→39.97 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.642 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.075 / 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
Rfree0.19138 3777 5 %RANDOM
Rwork0.16331 ---
obs0.16471 71247 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å20 Å2
2--2.72 Å20 Å2
3----1.76 Å2
Refinement stepCycle: LAST / Resolution: 1.57→39.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3619 0 142 362 4123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193969
X-RAY DIFFRACTIONr_bond_other_d0.0020.023589
X-RAY DIFFRACTIONr_angle_refined_deg1.7631.9775433
X-RAY DIFFRACTIONr_angle_other_deg0.79538234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15526.061165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.91915531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.78158
X-RAY DIFFRACTIONr_chiral_restr0.1050.2583
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214702
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02929
X-RAY DIFFRACTIONr_nbd_refined0.2430.21041
X-RAY DIFFRACTIONr_nbd_other0.1770.23398
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21971
X-RAY DIFFRACTIONr_nbtor_other0.0810.21894
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2113
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0050.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1150.216
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.2370
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2140.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0390.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3391.9732001
X-RAY DIFFRACTIONr_mcbond_other1.3371.9732000
X-RAY DIFFRACTIONr_mcangle_it1.892.9562517
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2192.3691968
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: 1.57→1.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 268 -
Rwork0.241 5203 -
obs--99.65 %
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)
12.3759-0.5128-0.56562.42141.82563.2944-0.04990.4121-0.2538-0.2042-0.11190.23290.1481-0.34430.16180.1353-0.07140.00960.2482-0.06970.0706-12.407-2.5228-21.0704
21.3987-0.01210.30230.89260.62014.8816-0.00090.0495-0.17870.0067-0.0153-0.0660.51240.22290.01620.16410.01360.0460.1596-0.03790.04969.5177-6.094-22.0641
31.6524-0.14670.36841.03640.57155.4426-0.01890.0326-0.08640.0380.0687-0.14220.08110.3043-0.04980.01290.0231-0.00270.16520.02380.035713.07976.653516.2514
41.6711-0.6132-0.34182.33241.85354.2129-0.0783-0.0544-0.11640.0999-0.06660.12590.0811-0.16820.14480.00610.00090.00850.15930.00460.0127-8.437612.551416.1131
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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