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- PDB-6a56: AJLec from the Sea Anemone Anthopleura japonica -

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Basic information

Entry
Database: PDB / ID: 6a56
TitleAJLec from the Sea Anemone Anthopleura japonica
ComponentsAJLec
KeywordsSUGAR BINDING PROTEIN / AJLec / Lectin / Sea Anemone / Gyractis japonica
Function / homologycarbohydrate binding / beta-lactose / Galactose-specific lectin
Function and homology information
Biological speciesAnthopleura japonica (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsUnno, H. / Hatakeyama, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science15K06977 Japan
CitationJournal: Sci Rep / Year: 2018
Title: Identification, Characterization, and X-ray Crystallographic Analysis of a Novel Type of Lectin AJLec from the Sea Anemone Anthopleura japonica.
Authors: Unno, H. / Nakamura, A. / Mori, S. / Goda, S. / Yamaguchi, K. / Hiemori, K. / Tateno, H. / Hatakeyama, T.
History
DepositionJun 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / entity_poly / 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_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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.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.type / _entity_poly.pdbx_seq_one_letter_code_can / _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_comp_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_comp_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AJLec
B: AJLec
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0419
Polymers36,9582
Non-polymers1,0837
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-51 kcal/mol
Surface area14360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.079, 79.732, 106.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PCAPCAARGARGAA1 - 641 - 64
21PCAPCAARGARGBB1 - 641 - 64
12GLYGLYVALVALAA66 - 16466 - 164
22GLYGLYVALVALBB66 - 16466 - 164

NCS ensembles :
ID
1
2

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Components

#1: Protein AJLec


Mass: 18478.779 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Anthopleura japonica (sea anemone) / References: UniProt: A0A2Z5WLM1*PLUS
#2: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-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: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe sequence is based on GenBank: LC339819

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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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 100 mM lactose, 1 mM CaCl2, 200 mM NaCl, 100 mM HEPES (pH 7.5), 30% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.2→63.7 Å / Num. obs: 101402 / % possible obs: 99.7 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 25.6
Reflection shellResolution: 1.2→1.23 Å / Rmerge(I) obs: 0.243

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→22.08 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.42 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.039 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17638 5139 5.1 %RANDOM
Rwork0.14239 ---
obs0.14408 96187 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.806 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2---0.19 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.2→22.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2604 0 65 400 3069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0142809
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172339
X-RAY DIFFRACTIONr_angle_refined_deg1.8871.7013790
X-RAY DIFFRACTIONr_angle_other_deg1.1141.6875504
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2065334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.55521.831142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.14515408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.661514
X-RAY DIFFRACTIONr_chiral_restr0.120.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023096
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02572
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_it1.37210.5041318
X-RAY DIFFRACTIONr_mcbond_other1.37211.431317
X-RAY DIFFRACTIONr_mcangle_it1.561636
X-RAY DIFFRACTIONr_mcangle_other1.561637
X-RAY DIFFRACTIONr_scbond_it1.791.4071491
X-RAY DIFFRACTIONr_scbond_other1.791491
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other213.7332149
X-RAY DIFFRACTIONr_long_range_B_refined2.0993050
X-RAY DIFFRACTIONr_long_range_B_other2.0642968
X-RAY DIFFRACTIONr_rigid_bond_restr7.03832796
X-RAY DIFFRACTIONr_sphericity_free13.1855267
X-RAY DIFFRACTIONr_sphericity_bonded13.89552812
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A15590.17
12B15590.17
21A28500.12
22B28500.12
LS refinement shellResolution: 1.198→1.229 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 347 -
Rwork0.161 6429 -
obs--90.55 %

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