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- PDB-4usp: X-ray structure of the dimeric CCL2 lectin in native form -

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Basic information

Entry
Database: PDB / ID: 4usp
TitleX-ray structure of the dimeric CCL2 lectin in native form
ComponentsCCL2 LECTIN
KeywordsSUGAR BINDING PROTEIN / LECTIN / 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
PHOSPHATE ION / CCL2 lectin
Similarity search - Component
Biological speciesCOPRINOPSIS CINEREA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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
Revision 1.3May 3, 2017Group: Database references
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3394
Polymers33,2092
Non-polymers1302
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-10 kcal/mol
Surface area11830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.921, 59.921, 202.907
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.42841, -0.90358, 0.00148), (-0.90347, -0.42838, -0.01539), (0.01454, 0.00526, -0.99988)
Vector: 17.24904, 28.22673, 105.69557)

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Components

#1: Protein CCL2 LECTIN


Mass: 16604.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) COPRINOPSIS CINEREA (fungus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: B3GA02
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.75 Å3/Da / Density % sol: 55.3 % / Description: NONE
Crystal growpH: 7.5
Details: MIDAS 1-14 15% PENTAERYTHRITOL PROPOXYLATE 5/4 PO/OH 0.1M HEPES 7.50 0.2M SODIUM THIOCYANATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9205
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9205 Å / Relative weight: 1
ReflectionResolution: 2.25→44.85 Å / Num. obs: 18296 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.7
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.7 / % possible all: 99.8

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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 4USO

4uso


Resolution: 2.25→44.85 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 9.993 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.174 / 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
Rfree0.20997 892 4.9 %RANDOM
Rwork0.17223 ---
obs0.17414 17392 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.256 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20 Å20 Å2
2--1.25 Å20 Å2
3----2.51 Å2
Refinement stepCycle: LAST / Resolution: 2.25→44.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2066 0 6 195 2267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022124
X-RAY DIFFRACTIONr_bond_other_d0.0050.021948
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.942916
X-RAY DIFFRACTIONr_angle_other_deg1.03534470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3935268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29123.86488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19215308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.181514
X-RAY DIFFRACTIONr_chiral_restr0.0960.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212454
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02496
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_it0.8221.3191078
X-RAY DIFFRACTIONr_mcbond_other0.8151.3171077
X-RAY DIFFRACTIONr_mcangle_it1.3561.9691344
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5541.4171046
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: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 51 -
Rwork0.224 1292 -
obs--99.63 %
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)
12.50630.4905-0.0861.38290.18123.0041-0.0749-0.09520.0918-0.05120.0538-0.0549-0.0347-0.02040.02110.00550.01580.00680.13660.02350.099513.89599.381968.9775
21.4511-0.0852-1.23092.0180.21143.65460.00130.2454-0.0352-0.2155-0.02880.1060.132-0.59910.02750.1516-0.03170.00840.23650.03760.136614.808110.588636.9192
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 131
2X-RAY DIFFRACTION2B8 - 142

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