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- PDB-3d4k: Concanavalin A Complexed to a Synthetic Analog of the Trimannoside -

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Basic information

Entry
Database: PDB / ID: 3d4k
TitleConcanavalin A Complexed to a Synthetic Analog of the Trimannoside
ComponentsConcanavalin-A
KeywordsSUGAR BINDING PROTEIN / Concanavalin A / Conserved Water / Carbohydrate-Protein Binding / Glycoprotein / Lectin / Manganese / Metal-binding
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 ...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
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsKadirvelraj, R. / Foley, B.L. / Dyekjaer, J.D. / Woods, R.J.
Citation
Journal: J.Am.Chem.Soc. / Year: 2008
Title: Involvement of water in carbohydrate-protein binding: concanavalin A revisited.
Authors: Kadirvelraj, R. / Foley, B.L. / Dyekjaer, J.D. / Woods, R.J.
#1: Journal: J.Am.Chem.Soc. / Year: 2001
Title: Involvement of water in carbohydrate-protein binding.
Authors: Clarke, C. / Woods, R.J. / Gluska, J. / Cooper, A. / Nutley, M.A. / Boons, G.J.
#2: Journal: J.Biol.Chem. / Year: 1996
Title: Structural basis of trimannoside recognition by concanavalin A.
Authors: Naismith, J.H. / Field, R.A.
History
DepositionMay 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jun 7, 2017Group: Other / Source and taxonomy
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
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_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.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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.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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 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
B: Concanavalin-A
C: Concanavalin-A
D: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,42420
Polymers102,4904
Non-polymers2,93516
Water10,305572
1
A: Concanavalin-A
D: Concanavalin-A
hetero molecules

B: Concanavalin-A
C: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,42420
Polymers102,4904
Non-polymers2,93516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area13160 Å2
ΔGint-78 kcal/mol
Surface area33230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.015, 63.547, 126.215
Angle α, β, γ (deg.)90.000, 86.910, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Concanavalin-A / Con A


Mass: 25622.385 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Jack-bean / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P02866
#2: Polysaccharide
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]methyl 2-deoxy-2-(2-hydroxyethyl)-alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]methyl 2-deoxy-2-(2-hydroxyethyl)-alpha-D-mannopyranoside


Type: oligosaccharide / Mass: 546.518 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a1122h-1a_1-5_1*OC_2*CCO][a1122h-1a_1-5]/1-2-2/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-2-deoxy-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 584 molecules

#3: Chemical
ChemComp-MN / MANGANESE (II) ION


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


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / 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: 2.34 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 10-16% PEG 6000, 100 mM Sodium cacodylate, 50 mM NaCL, 1 mM MnCL2, 1 mM CaCL2, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.935 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 14, 2002 / Details: Mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.935 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. all: 88130 / Num. obs: 87296 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.036 / Χ2: 1.057 / Net I/σ(I): 13.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.01 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 2.9 / Num. unique all: 8649 / Rsym value: 0.502 / Χ2: 1.063 / % possible all: 98.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.576 / Cor.coef. Fo:Fc: 0.13 / Cor.coef. Io to Ic: 0.12
Highest resolutionLowest resolution
Rotation5 Å20 Å
Translation5 Å20 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1QD0

1qd0


Resolution: 1.8→30 Å / FOM work R set: 0.83 / Isotropic thermal model: Isotropic / Cross valid method: SigmaA / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 8749 9.9 %Random
Rwork0.205 ---
all0.221 88131 --
obs0.221 87269 99 %-
Solvent computationBsol: 52.702 Å2
Displacement parametersBiso mean: 24.552 Å2
Baniso -1Baniso -2Baniso -3
1-2.397 Å20 Å20.641 Å2
2---7.101 Å20 Å2
3---4.704 Å2
Refine analyzeLuzzati coordinate error obs: 0.223 Å / Luzzati d res low obs: 30 Å / Luzzati sigma a obs: 0.076 Å
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7236 0 180 572 7988
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.526
X-RAY DIFFRACTIONc_mcbond_it1.4271.5
X-RAY DIFFRACTIONc_scbond_it2.0082
X-RAY DIFFRACTIONc_mcangle_it2.2892
X-RAY DIFFRACTIONc_scangle_it3.0062.5
LS refinement shellResolution: 1.8→1.86 Å
RfactorNum. reflection% reflection
Rfree0.315 159 -
Rwork0.283 --
obs-1575 98.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2triman.paramtriman.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4water_rep.paramwater.top
X-RAY DIFFRACTION5glycerol.paramglycerol.top

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