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- PDB-3alt: Crystal structure of CEL-IV complexed with Melibiose -

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Basic information

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


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
alpha-melibiose / Lectin CEL-IV, C-type
Similarity search - Component
Biological speciesCucumaria echinata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.2Jan 29, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_symm_contact / 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.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _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 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _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

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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)69,96512
Polymers68,4354
Non-polymers1,5308
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7960 Å2
ΔGint-67 kcal/mol
Surface area25960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.988, 78.504, 102.898
Angle α, β, γ (deg.)90.00, 98.41, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A3 - 155
2111B3 - 155
3111C3 - 155
4111D3 - 155
1121A301
2121B301
3121C301
4121D301

NCS ensembles :
ID
1
2

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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 / alpha-melibiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-melibiose
DescriptorTypeProgram
DGalpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(6+1)][a-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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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: 2.57 Å3/Da / Density % sol: 52.06 %
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: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 7, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→41.9 Å / Num. obs: 22552 / % possible obs: 95.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 48.4 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 30.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 7 / % possible all: 92.4

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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: 1WMY

1wmy


Resolution: 2.5→38.06 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.873 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.771 / SU ML: 0.277 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.94 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1167 5.1 %RANDOM
Rwork0.229 21878 --
obs0.2316 21878 95.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 61.97 Å2 / Biso mean: 34.8777 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.5→38.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4788 0 96 93 4977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0215036
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.9356884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4045620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11124.667240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.73615688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7771516
X-RAY DIFFRACTIONr_chiral_restr0.1230.2740
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213920
X-RAY DIFFRACTIONr_mcbond_it0.7841.53080
X-RAY DIFFRACTIONr_mcangle_it1.53524912
X-RAY DIFFRACTIONr_scbond_it1.86731956
X-RAY DIFFRACTIONr_scangle_it3.0374.51972
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1172TIGHT POSITIONAL0.070.05
1B1172TIGHT POSITIONAL0.070.05
1C1172TIGHT POSITIONAL0.070.05
1D1172TIGHT POSITIONAL0.070.05
1A1172TIGHT THERMAL0.140.5
1B1172TIGHT THERMAL0.130.5
1C1172TIGHT THERMAL0.150.5
1D1172TIGHT THERMAL0.140.5
2A23TIGHT POSITIONAL0.060.05
2B23TIGHT POSITIONAL0.060.05
2C23TIGHT POSITIONAL0.060.05
2D23TIGHT POSITIONAL0.090.05
2A23TIGHT THERMAL0.140.5
2B23TIGHT THERMAL0.180.5
2C23TIGHT THERMAL0.160.5
2D23TIGHT THERMAL0.150.5
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 78 -
Rwork0.39 1559 -
all-1637 -
obs--92.38 %

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