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- PDB-5kxe: Wisteria floribunda lectin in complex with GalNAc(beta1-4)GlcNAc ... -

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Basic information

Entry
Database: PDB / ID: 5kxe
TitleWisteria floribunda lectin in complex with GalNAc(beta1-4)GlcNAc (LacdiNAc) at pH 4.2
ComponentsWisteria floribunda agglutinin
Keywordssugar binding protein/inhibitor / Carbohydrate-binding protein / lectin / sugar binding protein-inhibitor complex
Function / homology
Function and homology information


carbohydrate binding / metal ion binding
Similarity search - Function
Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily ...Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-6Y2 / : / PHOSPHATE ION / Wisteria floribunda agglutinin
Similarity search - Component
Biological speciesWisteria floribunda (Japanese wisteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å
AuthorsEvans, S.V. / Haji-Ghassemi, O.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)Discovery Grant, 171356-2013 Canada
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Molecular Basis for Recognition of the Cancer Glycobiomarker, LacdiNAc (GalNAc[ beta 14]GlcNAc), by Wisteria floribunda Agglutinin.
Authors: Haji-Ghassemi, O. / Gilbert, M. / Spence, J. / Schur, M.J. / Parker, M.J. / Jenkins, M.L. / Burke, J.E. / van Faassen, H. / Young, N.M. / Evans, S.V.
History
DepositionJul 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Nov 23, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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_conn_angle / pdbx_validate_close_contact / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 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 / 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_conn.pdbx_leaving_atom_flag / _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: Wisteria floribunda agglutinin
B: Wisteria floribunda agglutinin
C: Wisteria floribunda agglutinin
D: Wisteria floribunda agglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,82427
Polymers106,7784
Non-polymers6,04723
Water10,233568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11740 Å2
ΔGint-96 kcal/mol
Surface area37900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.584, 97.943, 149.158
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 31 - 268 / Label seq-ID: 1 - 238

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Wisteria floribunda agglutinin


Mass: 26694.438 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Wisteria floribunda (Japanese wisteria) / Plasmid details: seed lectin / References: UniProt: A0A1D5B395*PLUS

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Sugars , 3 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4/a3-b1_a4-c1_c4-d1_d6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D- ...beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1189.079 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-2[DManpa1-3][DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a212h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4-5-5/a3-b1_a4-c1_c4-d1_d2-e1_d3-f1_d6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(2+1)][b-D-Xylp]{}[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 6 types, 587 molecules

#5: Chemical
ChemComp-6Y2 / ~{N}-[(2~{S},3~{R},4~{R},5~{R},6~{R})-2-[(2~{R},3~{S},4~{R},5~{R},6~{S})-5-acetamido-2-(hydroxymethyl)-6-(4-nitrophenoxy)-4-oxidanyl-oxan-3-yl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]ethanamide


Mass: 545.494 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H31N3O13
#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#9: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 2.67 Å3/Da / Density % sol: 53.98 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2 M Lithium Sulfate 0.1 M phosphate-citrate pH 4.2 20% (w/v) PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 11, 2015 / Details: Vertical Focusing Mirror
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.09→50.01 Å / Num. obs: 67430 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.057 / Rrim(I) all: 0.156 / Χ2: 0.925 / Net I/av σ(I): 17.476 / Net I/σ(I): 5.9 / Num. measured all: 502533
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2
2.09-2.157.50.77455480.860.3050.8330.981
2.15-2.227.50.68955380.90.2710.7410.991
2.22-2.37.50.50255400.920.1970.540.974
2.3-2.397.50.50655720.930.1990.5440.956
2.39-2.57.50.42755360.9420.1680.4590.92
2.5-2.637.50.35655840.9610.140.3830.92
2.63-2.87.50.24655870.9760.0960.2640.91
2.8-3.017.50.1755790.9890.0670.1830.891
3.01-3.327.50.10556400.9940.0410.1120.887
3.32-3.87.50.06256630.9970.0240.0670.9
3.8-4.787.40.04157050.9990.0160.0440.886
4.78-307.10.03859380.9990.0150.0410.891

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.82 Å29.91 Å
Translation7.82 Å29.91 Å

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Processing

Software
NameVersionClassification
REFMACrefinement
HKL-2000data scaling
PHASER2.6.1phasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KXC

5kxc


Resolution: 2.09→50.01 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.1822 / WRfactor Rwork: 0.1517 / FOM work R set: 0.8546 / SU B: 4.433 / SU ML: 0.115 / SU R Cruickshank DPI: 0.1982 / SU Rfree: 0.1621 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2117 3413 5.1 %RANDOM
Rwork0.1806 ---
obs0.1822 63779 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.78 Å2 / Biso mean: 28.467 Å2 / Biso min: 14.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.42 Å2
Refinement stepCycle: final / Resolution: 2.09→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7404 0 383 568 8355
Biso mean--59.29 33.25 -
Num. residues----952
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.027988
X-RAY DIFFRACTIONr_bond_other_d0.0020.027197
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.99210964
X-RAY DIFFRACTIONr_angle_other_deg0.9913.00916670
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1685948
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66725.116344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.627151152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.331520
X-RAY DIFFRACTIONr_chiral_restr0.1790.21319
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218794
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021750
X-RAY DIFFRACTIONr_mcbond_it1.5672.5583804
X-RAY DIFFRACTIONr_mcbond_other1.5662.5563803
X-RAY DIFFRACTIONr_mcangle_it2.4413.8234748
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A156280.04
12B156280.04
21A156140.05
22C156140.05
31A156920.05
32D156920.05
41B156400.05
42C156400.05
51B156380.04
52D156380.04
61C156120.06
62D156120.06
LS refinement shellResolution: 2.087→2.141 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 248 -
Rwork0.221 4546 -
all-4794 -
obs--97.52 %

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