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- PDB-4uso: X-ray structure of the CCL2 lectin in complex with sialyl lewis X -

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Basic information

Entry
Database: PDB / ID: 4uso
TitleX-ray structure of the CCL2 lectin in complex with sialyl lewis X
ComponentsCCL2 LECTIN
KeywordsSUGAR BINDING PROTEIN / DIMERIC / FUNGAL
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
: / CCL2 lectin-like / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Sialyl-Lewis X antigen, beta anomer / CCL2 lectin
Similarity search - Component
Biological speciesCOPRINOPSIS CINEREA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBleuler-Martinez, S. / Varrot, A. / Schubert, M. / Stutz, M. / Sieber, R. / Hengartner, M. / Aebi, M. / Kunzler, M.
CitationJournal: Glycobiology / Year: 2017
Title: Dimerization of the fungal defense lectin CCL2 is essential for its toxicity against nematodes.
Authors: Bleuler-Martinez, S. / Stutz, K. / Sieber, R. / Collot, M. / Mallet, J.M. / Hengartner, M. / Schubert, M. / Varrot, A. / Kunzler, M.
History
DepositionJul 11, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Structure summary
Revision 1.2Jan 25, 2017Group: Database references / Other / Refinement description
Revision 1.3May 3, 2017Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CCL2 LECTIN
B: CCL2 LECTIN
C: CCL2 LECTIN
D: CCL2 LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2385
Polymers66,4174
Non-polymers8211
Water4,125229
1
A: CCL2 LECTIN
B: CCL2 LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0293
Polymers33,2092
Non-polymers8211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint5.2 kcal/mol
Surface area11660 Å2
MethodPISA
2
C: CCL2 LECTIN
D: CCL2 LECTIN


Theoretical massNumber of molelcules
Total (without water)33,2092
Polymers33,2092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-6.1 kcal/mol
Surface area11120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.680, 121.680, 144.907
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2051-

HOH

21A-2072-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.03128, 0.01844, -0.99934), (-0.01426, -0.99974, -0.01801), (-0.99941, 0.01369, 0.03154)1.44805, 198.22665, 1.6779
2given(-0.48228, -0.87599, 0.00716), (0.87583, -0.48233, -0.01665), (0.01804, -0.00175, 0.99984)65.36636, 178.56227, -23.23748
3given(0.04458, 0.88287, 0.46749), (-0.02716, 0.46885, -0.88286), (-0.99864, 0.02667, 0.04488)-108.45669, 86.79292, -24.01003

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Components

#1: Protein
CCL2 LECTIN


Mass: 16604.281 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) COPRINOPSIS CINEREA (fungus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: B3GA02
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose / Sialyl-Lewis X antigen / beta anomer


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 820.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Sialyl-Lewis X antigen, beta anomer
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4[LFucpa1-3]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-4/a3-b1_a4-c1_c3-d2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST 12 AMINO ACIDS ARE FROM THE NTERMINAL HISTAG

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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: 2.34 Å3/Da / Density % sol: 47.42 % / Description: NONE
Crystal growpH: 8.5
Details: MIDAS 2-28. 30% GLYCEROL ETHOXYLATE AND 0.1M TRIS PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9732
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Sep 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9732 Å / Relative weight: 1
ReflectionResolution: 1.95→29.23 Å / Num. obs: 46087 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18
Reflection shellResolution: 1.95→2 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2LIE

2lie


Resolution: 1.95→29.85 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.773 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED LOCAL NCS DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20433 2327 5 %RANDOM
Rwork0.17504 ---
obs0.1765 43754 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.158 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å2-0.42 Å20 Å2
2---0.84 Å20 Å2
3---2.74 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3991 0 56 229 4276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.024166
X-RAY DIFFRACTIONr_bond_other_d0.0080.023751
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9495735
X-RAY DIFFRACTIONr_angle_other_deg1.31238585
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3865530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01824.036166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.93415563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4761525
X-RAY DIFFRACTIONr_chiral_restr0.0940.2654
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214812
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02957
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3761.8152129
X-RAY DIFFRACTIONr_mcbond_other1.3761.8152128
X-RAY DIFFRACTIONr_mcangle_it2.0582.7072656
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7462.0122037
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: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 186 -
Rwork0.224 3168 -
obs--99.85 %
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)
12.3421-1.15240.84393.2331-0.76752.53220.0085-0.02190.0896-0.0671-0.0435-0.18280.1311-0.02680.03510.06070.00740.00220.04950.00260.0108-39.9888112.179631.5762
23.4452-1.17650.62443.8371-0.97832.80840.0657-0.3759-0.35470.0107-0.0467-0.35590.54860.2137-0.0190.37170.051-0.04980.18740.09160.2188-26.991286.030443.9629
33.23031.19510.45464.06570.64572.1529-0.0730.1479-0.4686-0.12910.1288-0.70450.2380.5955-0.05590.15890.020.05510.43750.06620.5418-14.142589.45637.863
41.92581.2550.57433.2810.73232.6436-0.0318-0.1769-0.03110.33250.04860.0511-0.09470.2553-0.01680.2025-0.0721-0.0620.69350.03320.6254.0089112.471519.6269
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 142
2X-RAY DIFFRACTION2B8 - 142
3X-RAY DIFFRACTION3C10 - 141
4X-RAY DIFFRACTION4D11 - 142

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