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- PDB-3alu: Crystal structure of CEL-IV complexed with Raffinose -

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Basic information

Entry
Database: PDB / ID: 3alu
TitleCrystal structure of CEL-IV complexed with Raffinose
ComponentsLectin CEL-IV, C-type
KeywordsSUGAR BINDING PROTEIN / CEL-IV / C-type lectin / Raffinose
Function / homology
Function and homology information


signaling receptor activity / metal ion binding
Similarity search - Function
: / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
raffinose / Lectin CEL-IV, C-type
Similarity search - Component
Biological speciesCucumaria echinata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHatakeyama, T. / Hozawa, T. / Ishii, K. / Kamiya, T. / Goda, S. / Kusunoki, M. / Unno, H.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Galactose recognition by a tetrameric C-type lectin, CEL-IV, containing the EPN carbohydrate recognition motif
Authors: Hatakeyama, T. / Kamiya, T. / Kusunoki, M. / Nakamura-Tsuruta, S. / Hirabayashi, J. / Goda, S. / Unno, H.
History
DepositionAug 7, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 30, 2012Group: Non-polymer description
Revision 1.3Jan 29, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_conn_angle / struct_asym / struct_conn / struct_conn_type / 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.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lectin CEL-IV, C-type
B: Lectin CEL-IV, C-type
C: Lectin CEL-IV, C-type
D: Lectin CEL-IV, C-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,17221
Polymers68,4354
Non-polymers2,73717
Water13,439746
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint-74 kcal/mol
Surface area25380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.808, 78.159, 102.883
Angle α, β, γ (deg.)90.00, 96.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Lectin CEL-IV, C-type


Mass: 17108.805 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cucumaria echinata (invertebrata) / References: UniProt: Q7M4F9
#2: Polysaccharide
alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose-(1-2)-beta-D-fructofuranose / raffinose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: raffinose
DescriptorTypeProgram
DGalpa1-6DGlcpa1-2DFrufbGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[ha122h-2b_2-5][a2122h-1a_1-5][a2112h-1a_1-5]/1-2-3/a2-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{[(6+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 746 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 4.3M NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 2, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→102.2 Å / Num. obs: 74625 / % possible obs: 95.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 19.562 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 29.4
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 2.8 / % possible all: 89.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WMY

1wmy


Resolution: 1.65→40.16 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.694 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 3742 5 %RANDOM
Rwork0.16474 ---
obs0.16663 70881 94.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.378 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→40.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4812 0 176 746 5734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0215137
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.9497014
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0325624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86724.667240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64315692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9241516
X-RAY DIFFRACTIONr_chiral_restr0.2420.2760
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213936
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9721.53100
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8324944
X-RAY DIFFRACTIONr_scbond_it2.74232037
X-RAY DIFFRACTIONr_scangle_it4.0854.52070
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.653→1.696 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 270 -
Rwork0.292 4654 -
obs--85.46 %

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