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- PDB-5wey: Joint X-ray/neutron structure of Concanavalin A with alpha1-2 D-m... -

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Basic information

Entry
Database: PDB / ID: 5wey
TitleJoint X-ray/neutron structure of Concanavalin A with alpha1-2 D-mannobiose
ComponentsConcanavalin-A
KeywordsSUGAR BINDING PROTEIN / Lectin / carbohydrate complex / protonation state / hydrogen bonding / neutron crystallography
Function / homology
Function and homology information


regulation of defense response to virus / D-mannose binding / defense response / 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
2alpha-alpha-mannobiose / DEUTERATED WATER / : / Concanavalin-A
Similarity search - Component
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKovalevsky, A. / Gerlits, O.O. / Woods, R.J.
Citation
Journal: Biochemistry / Year: 2017
Title: Mannobiose Binding Induces Changes in Hydrogen Bonding and Protonation States of Acidic Residues in Concanavalin A As Revealed by Neutron Crystallography.
Authors: Gerlits, O.O. / Coates, L. / Woods, R.J. / Kovalevsky, A.
#1: Journal: Acta Cryst. / Year: 2009
Title: Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules
Authors: Adams, P.D. / Mustyakimov, M. / Afonine, P.V. / Langan, P.
History
DepositionJul 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / 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 / refine_hist / 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.type / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_low
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 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: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0604
Polymers25,6221
Non-polymers4373
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: known assembly
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-20 kcal/mol
Surface area10720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.563, 86.618, 91.808
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Concanavalin-A / Con A


Mass: 25622.385 Da / Num. of mol.: 1 / Fragment: unp residues 164-281; unp residues 30-148 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P02866
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose / 2alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 2alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.5852.37
2
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 10% PEG 6K, 0.1 M sodium citrate, pH 5 in H2O

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22932
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.54
NUCLEAR REACTORORNL High Flux Isotope Reactor CG4D22.8-4.5
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV++1IMAGE PLATEJul 13, 2015
MAATEL IMAGINE2IMAGE PLATEFeb 3, 2017
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
22.81
34.51
Reflection
Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Entry-IDDiffraction-IDNet I/σ(I)
1.8-502339593.74.15WEY125.1
2.5-53.84773982.54.45WEY24.1

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Processing

SoftwareName: nCNS / Version: 1.0.0 / Classification: refinement
Refinement

% reflection Rfree: 5 % / R Free selection details: RANDOM / Cross valid method: FREE R-VALUE / σ(F): 2.5 / Stereochemistry target values: JOINT X-RAY/NEUTRON ML

Method to determine structureStarting modelResolution (Å)Refine-IDBiso max (Å2)Biso mean (Å2)Biso min (Å2)Rfactor RfreeRfactor RworkNum. reflection RfreeNum. reflection obs% reflection obs (%)
MOLECULAR REPLACEMENT1I3H

1i3h

1.8-40X-RAY DIFFRACTION77.0725.03439.990.2120.1919711974984.8
2.5-40NEUTRON DIFFRACTION0.2850.247303661469.6
Refinement stepCycle: LAST / Resolution: 1.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 25 139 1973
LS refinement shell

Total num. of bins used: 8 / % reflection Rfree: 5 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDRfactor Rfree errorNum. reflection all% reflection obs (%)
1.8-1.880.25620.251132X-RAY DIFFRACTION0.032119436.8
2.5-2.610.392260.356568NEUTRON DIFFRACTION0.07759448.5

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