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- PDB-2z49: Crystal Structure of Hemolytic Lectin CEL-III Complexed with meth... -

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Basic information

Entry
Database: PDB / ID: 2z49
TitleCrystal Structure of Hemolytic Lectin CEL-III Complexed with methyl-alpha-D-galactopylanoside
ComponentsHemolytic lectin CEL-III
KeywordsTOXIN / Lectin / CEL-III / Hemolysis / Hemagglutination / Pore-forming / Calcium / Magnesium / METHYL-ALPHA-D-GALACTOPYLANOSIDE
Function / homology
Function and homology information


positive regulation of erythrocyte aggregation / melibiose binding / cell killing / N-acetylgalactosamine binding / polypeptide N-acetylgalactosaminyltransferase activity / fucose binding / disruption of plasma membrane integrity in another organism / lactose binding / hemolysis in another organism / galactose binding ...positive regulation of erythrocyte aggregation / melibiose binding / cell killing / N-acetylgalactosamine binding / polypeptide N-acetylgalactosaminyltransferase activity / fucose binding / disruption of plasma membrane integrity in another organism / lactose binding / hemolysis in another organism / galactose binding / protein O-linked glycosylation / protein homooligomerization / antibacterial humoral response / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / calcium ion binding / Golgi apparatus / magnesium ion binding / extracellular space
Similarity search - Function
hemolytic lectin cel-iii, domain 3 / Hemolytic lectin CEL-III, C-terminal domain / Hemolytic lectin CEL-III, C-terminal domain superfamily / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) ...hemolytic lectin cel-iii, domain 3 / Hemolytic lectin CEL-III, C-terminal domain / Hemolytic lectin CEL-III, C-terminal domain superfamily / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
methyl alpha-D-galactopyranoside / Galactose/N-acetylgalactosamine-binding lectin CEL-III
Similarity search - Component
Biological speciesCucumaria echinata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHatakeyama, T. / Unno, H. / Eto, S. / Hidemura, H. / Uchida, T. / Kouzuma, Y.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: C-type lectin-like carbohydrate-recognition of the hemolytic lectin CEL-III containing ricin-type beta-trefoil folds
Authors: Hatakeyama, T. / Unno, H. / Kouzuma, Y. / Uchida, T. / Eto, S. / Hidemura, H. / Kato, N. / Yonekura, M. / Kusunoki, M.
History
DepositionJun 13, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence / Category: entity_poly / pdbx_struct_mod_residue
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id
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.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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 2.2Nov 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemolytic lectin CEL-III
B: Hemolytic lectin CEL-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,34426
Polymers94,9042
Non-polymers2,44024
Water13,331740
1
A: Hemolytic lectin CEL-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,67213
Polymers47,4521
Non-polymers1,22012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hemolytic lectin CEL-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,67213
Polymers47,4521
Non-polymers1,22012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.287, 65.451, 126.993
Angle α, β, γ (deg.)90.00, 97.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hemolytic lectin CEL-III


Mass: 47452.164 Da / Num. of mol.: 2 / Fragment: residues in database 11-442 / Source method: isolated from a natural source / Source: (natural) Cucumaria echinata (invertebrata) / References: UniProt: Q868M7
#2: Sugar
ChemComp-AMG / methyl alpha-D-galactopyranoside / ALPHA-METHYL-D-GALACTOSIDE / methyl alpha-D-galactoside / methyl D-galactoside / methyl galactoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
IdentifierTypeProgram
DGalp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-methyl-galactosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 740 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE ARE 13 DIFFERENCES BETWEEN THE DEPOSITORS DATA AND THE GENETIC SEQUENCE. THERE IS NO QUESTION ...THERE ARE 13 DIFFERENCES BETWEEN THE DEPOSITORS DATA AND THE GENETIC SEQUENCE. THERE IS NO QUESTION FROM THE ELECTRON DENSITY THAT THESE RESIDUES ARE NOT DATABASE SEQUENCE. THE DEPOSITORS THINK THAT THERE ARE SEVERAL ISOPROTEINS.

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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: 2.32 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10mM METHYL-ALPHA-D-GALACTOPYLANOSIDE, 12% PEG 8000, 100mM Bis-Tris/NaOH, 200mM magnesium acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: BRUKER DIP-6040B / Detector: IMAGE PLATE / Date: Oct 2, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.95→125.99 Å / Num. obs: 63509 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 14.1
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VCL

1vcl


Resolution: 1.95→58.12 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.296 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23926 3221 5.1 %RANDOM
Rwork0.19061 ---
obs0.19311 60266 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.578 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.95→58.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6618 0 144 740 7502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226893
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.9589371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5095861
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.90625.482332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.598151096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8271536
X-RAY DIFFRACTIONr_chiral_restr0.0930.21043
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025240
X-RAY DIFFRACTIONr_nbd_refined0.2110.23312
X-RAY DIFFRACTIONr_nbtor_refined0.3010.24758
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2736
X-RAY DIFFRACTIONr_metal_ion_refined0.090.240
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.229
X-RAY DIFFRACTIONr_mcbond_it0.771.54348
X-RAY DIFFRACTIONr_mcangle_it1.27626855
X-RAY DIFFRACTIONr_scbond_it1.91932895
X-RAY DIFFRACTIONr_scangle_it2.9974.52516
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 194 -
Rwork0.221 4477 -
obs--100 %

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