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- PDB-5av7: Crystal structure of Calsepa lectin in complex with bisected glycan -

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Basic information

Entry
Database: PDB / ID: 5av7
TitleCrystal structure of Calsepa lectin in complex with bisected glycan
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / Lectin / glycan
Function / homology
Function and homology information


glucose binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / mannose binding / cell adhesion molecule binding / positive regulation of mitotic nuclear division / carbohydrate binding / protein homodimerization activity / identical protein binding / cytoplasm
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
Jacalin-related lectin Calsepa
Similarity search - Component
Biological speciesCalystegia sepium (hedge bindweed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsNagae, M. / Yamaguchi, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
MEXT15K18496, 26110724 Japan
CitationJournal: Sci Rep / Year: 2016
Title: Atomic visualization of a flipped-back conformation of bisected glycans bound to specific lectins
Authors: Nagae, M. / Kanagawa, M. / Morita-Matsumoto, K. / Hanashima, S. / Kizuka, Y. / Taniguchi, N. / Yamaguchi, Y.
History
DepositionJun 12, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations / Category: chem_comp / diffrn_source / pdbx_struct_oper_list
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 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_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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.auth_asym_id / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_mod_residue.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lectin
B: Lectin
C: Lectin
D: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7466
Polymers63,4904
Non-polymers2,2562
Water3,729207
1
A: Lectin
B: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8733
Polymers31,7452
Non-polymers1,1281
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Lectin
D: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8733
Polymers31,7452
Non-polymers1,1281
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.608, 52.836, 54.774
Angle α, β, γ (deg.)90.01, 90.03, 94.05
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Lectin /


Mass: 15872.536 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Calystegia sepium (hedge bindweed) / Production host: Escherichia coli (E. coli) / References: UniProt: P93114
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)][2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]methyl alpha-D-mannopyranoside


Type: oligosaccharide / Mass: 1128.042 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6][DGlcpNAcb1-4]DManp[1Me]a1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a1122h-1a_1-5_1*OC][a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2-3-3-2-3/a3-b1_a4-d1_a6-e1_b2-c1_e2-f1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Hepes-Na (pH 7.5), 3.0 M NaCl

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→100 Å / Num. obs: 44270 / % possible obs: 97 % / Redundancy: 1.9 % / Rsym value: 0.088 / Net I/σ(I): 16.7
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 2 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 1.9 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OUW

1ouw


Resolution: 1.85→54.77 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.307 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27877 2234 5.1 %RANDOM
Rwork0.24542 ---
obs0.24712 41846 96.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.096 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-1.66 Å2-0.05 Å2
2---0.09 Å2-0.1 Å2
3---0.64 Å2
Refinement stepCycle: 1 / Resolution: 1.85→54.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4335 0 154 207 4696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.024597
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0791.9746262
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9915574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.39724.439187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64515635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8481516
X-RAY DIFFRACTIONr_chiral_restr0.0670.2718
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213462
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_it1.0962.2732326
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9343.4012890
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0152.3182271
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.82419.1256956
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 151 -
Rwork0.289 3125 -
obs--95.99 %

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