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- PDB-2z48: Crystal Structure of Hemolytic Lectin CEL-III Complexed with GalNac -

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Basic information

Entry
Database: PDB / ID: 2z48
TitleCrystal Structure of Hemolytic Lectin CEL-III Complexed with GalNac
ComponentsHemolytic lectin CEL-III
KeywordsTOXIN / Lectin / CEL-III / Hemolysis / Hemagglutination / Pore-forming / Calcium / Magnesium / GalNac
Function / homology
Function and homology information


positive regulation of erythrocyte aggregation / melibiose binding / lactose binding / cell killing / N-acetylgalactosamine binding / fucose binding / disruption of plasma membrane integrity in another organism / galactose binding / hemolysis in another organism / protein homooligomerization ...positive regulation of erythrocyte aggregation / melibiose binding / lactose binding / cell killing / N-acetylgalactosamine binding / fucose binding / disruption of plasma membrane integrity in another organism / galactose binding / hemolysis in another organism / protein homooligomerization / : / antibacterial humoral response / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / calcium ion binding / 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
2-acetamido-2-deoxy-alpha-D-galactopyranose / 2-acetamido-2-deoxy-beta-D-galactopyranose / Galactose/N-acetylgalactosamine-binding lectin CEL-III
Similarity search - Component
Biological speciesCucumaria echinata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.2Jul 25, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / entity_src_nat / Item: _entity.pdbx_mutation / _entity.src_method
Revision 2.0Dec 25, 2019Group: Data collection / Database references / Polymer sequence
Category: chem_comp / entity_poly / struct_ref_seq_dif
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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 3.1Nov 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)98,05728
Polymers94,9042
Non-polymers3,15226
Water15,097838
1
A: Hemolytic lectin CEL-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,02814
Polymers47,4521
Non-polymers1,57613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hemolytic lectin CEL-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,02814
Polymers47,4521
Non-polymers1,57613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.637, 65.169, 66.675
Angle α, β, γ (deg.)85.30, 73.55, 89.94
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 1 / Auth seq-ID: 2 - 432 / Label seq-ID: 2 - 432

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hemolytic lectin CEL-III


Mass: 47452.164 Da / Num. of mol.: 2 / Fragment: residues in database 11-442 / Mutation: Q11PCA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cucumaria echinata (invertebrata) / Production host: Escherichia coli / References: UniProt: Q868M7

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Sugars , 2 types, 12 molecules

#2: Sugar
ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE / N-Acetylgalactosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar
ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE / N-Acetylgalactosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 852 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 838 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10mM GalNac, 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: 1.7→64.96 Å / Num. obs: 89844 / % possible obs: 96.4 % / Redundancy: 2 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 10.6
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 3.5 / % possible all: 95.2

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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: 1.7→64.96 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.14 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21752 4489 5 %RANDOM
Rwork0.18455 ---
obs0.18618 85355 96.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.532 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→64.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6610 0 194 838 7642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226934
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9659430
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6525860
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.89725.482332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.078151096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1321536
X-RAY DIFFRACTIONr_chiral_restr0.1050.21052
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025292
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.23350
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.24778
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2701
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0580.236
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.283
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.258
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8661.54345
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3426844
X-RAY DIFFRACTIONr_scbond_it2.17832950
X-RAY DIFFRACTIONr_scangle_it3.3044.52586
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3306 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.080.05
tight thermal0.230.5
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 359 -
Rwork0.225 6188 -
obs--95.04 %

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