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

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Basic information

Entry
Database: PDB / ID: 5kxd
TitleWisteria floribunda lectin in complex with GalNAc(beta1-4)GlcNAc (LacdiNAc) at pH 6.5
ComponentsWisteria floribunda agglutinin
KeywordsSUGAR BINDING PROTEIN / Carbohydrate-binding protein / lectin
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 / Jelly Rolls ...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 / ACETATE ION / : / Wisteria floribunda agglutinin
Similarity search - Component
Biological speciesWisteria floribunda (Japanese wisteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 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 1.4Nov 22, 2017Group: Database references / Category: pdbx_database_related
Revision 1.5Jan 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: 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_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 / _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 / _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)111,83526
Polymers106,7744
Non-polymers5,06122
Water11,476637
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11260 Å2
ΔGint-68 kcal/mol
Surface area37210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.096, 104.271, 148.739
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: 0 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / 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: 26693.451 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Wisteria floribunda (Japanese wisteria) / Plasmid details: seed lectin / References: UniProt: A0A1D5B396*PLUS

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Sugars , 3 types, 4 molecules

#2: 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
#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
#8: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 655 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#6: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#7: 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
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 637 / 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: 2.93 Å3/Da / Density % sol: 58.03 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M NaAc 0.1 M MES pH 6.5 30% (w/v) PEG 400

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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: 1.95→30 Å / Num. obs: 89308 / % possible obs: 99.3 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.089 / Rrim(I) all: 0.185 / Χ2: 0.907 / Net I/av σ(I): 15.712 / Net I/σ(I): 5.7 / Num. measured all: 669044
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.95-2.017.673050.7820.5080.94398.6
2.01-2.077.673130.820.3970.95898.9
2.07-2.157.673260.8770.3180.96298.80.8240.884
2.15-2.237.673420.920.2460.95399.10.6370.683
2.23-2.337.673930.940.2020.9499.10.5240.562
2.33-2.467.673500.9530.170.92599.20.4410.473
2.46-2.617.674170.9610.1360.91299.30.3510.376
2.61-2.817.574300.9760.0940.91599.40.2430.261
2.81-3.097.574720.9870.0610.91999.50.1570.168
3.09-3.547.475060.9950.0320.89599.60.0830.089
3.54-4.467.375730.9970.0180.79299.80.0450.049
4.46-257.178810.9980.0140.76799.90.0350.037

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KXC

5kxc


Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.195 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1981 4358 4.9 %RANDOM
Rwork0.1789 ---
obs0.1798 84025 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.8 Å2 / Biso mean: 22.833 Å2 / Biso min: 10.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.7 Å2
Refinement stepCycle: final / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7404 0 326 637 8367
Biso mean--41.9 29.9 -
Num. residues----952
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.027928
X-RAY DIFFRACTIONr_bond_other_d0.0030.027190
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.98210865
X-RAY DIFFRACTIONr_angle_other_deg0.9983.00916629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9275948
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91925.116344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.767151152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6691520
X-RAY DIFFRACTIONr_chiral_restr0.1790.21298
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218821
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021757
X-RAY DIFFRACTIONr_mcbond_it1.482.023810
X-RAY DIFFRACTIONr_mcbond_other1.4662.0173803
X-RAY DIFFRACTIONr_mcangle_it2.3113.0144748
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A154780.07
12B154780.07
21A154100.07
22C154100.07
31A154280.07
32D154280.07
41B153080.07
42C153080.07
51B155740.05
52D155740.05
61C153320.08
62D153320.08
LS refinement shellResolution: 1.952→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 283 -
Rwork0.22 5799 -
all-6082 -
obs--92.56 %

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