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- PDB-1qdc: MAN(APLHA1-6)MAN(ALPHA1-O)METHYL CONCANAVALIN A COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1qdc
TitleMAN(APLHA1-6)MAN(ALPHA1-O)METHYL CONCANAVALIN A COMPLEX
ComponentsPROTEIN (CONCANAVALIN A)
KeywordsSUGAR BINDING PROTEIN / PLANT LECTIN / CARBOHYDRATE BINDING / DIMANNOSE / CONCANAVALIN A
Function / homology
Function and homology information


D-mannose binding / toxin activity / metal ion binding
Similarity search - Function
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBouckaert, J. / Loris, R. / Wyns, L.
Citation
Journal: J.Biol.Chem. / Year: 1999
Title: The crystal structures of Man(alpha1-3)Man(alpha1-O)Me and Man(alpha1-6)Man(alpha1-O)Me in complex with concanavalin A.
Authors: Bouckaert, J. / Hamelryck, T.W. / Wyns, L. / Loris, R.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: Concanavalin a Crystallized in Complex with the Trisaccharide 3,6-Di-O-(Alpha- D-Mannopyranosyl)-Alpha-D-Mannopyranoside
Authors: Loris, R. / Maes, D. / Poortmans, F. / Wyns, L. / Bouckaert, J.
#2: Journal: J.Biol.Chem. / Year: 1996
Title: Structural Basis of Trimannoside Recognition by Concanavalin A
Authors: Naismith, J.H. / Field, R.A.
#3: Journal: Biochemistry / Year: 1994
Title: Thermodynamics of Lectin-Carbohydrate Interactions. Titration Microcalorimetry Measurements of the Binding of N-Linked Carbohydrates and Ovalbumin to concanavalin A
Authors: Mandal, D.K. / Kishore, N. / Brewer, C.F.
History
DepositionJul 14, 1998Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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_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.mon_nstd_flag / _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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 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: PROTEIN (CONCANAVALIN A)
B: PROTEIN (CONCANAVALIN A)
C: PROTEIN (CONCANAVALIN A)
D: PROTEIN (CONCANAVALIN A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,33017
Polymers102,4904
Non-polymers1,84113
Water6,954386
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.510, 117.03, 120.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsTHE ASYMMETRIC UNIT CONTAINS A TETRAMER, COMPOSED OF IDENTICAL MONOMERS OF 237 AMINO ACIDS. THE FOLLOWING RESIDUES ARE IN WEAK ELECTRON DENSITY: 118 AND 119, 150 AND 151, 161 AND 162.

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
PROTEIN (CONCANAVALIN A) / CON A


Mass: 25622.385 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: CO-CRYSTALS OF CONCANAVALIN A WITH METHYL-6--O-(ALPHA-D-MANNOPYRANOSYL)-ALPHA- D-MANNOPYRANOSIDE
Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P55915
#2: Polysaccharide
alpha-D-mannopyranose-(1-6)-methyl alpha-D-mannopyranoside


Type: oligosaccharide / Mass: 356.323 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManp[1Me]a1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1a_1-5_1*OC][a1122h-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 395 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.38 Å3/Da / Density % sol: 39.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: DROP: 5 MICROLITER 7 MG/ML CON A + 5 MICROLITER 7% JEFFAMINE M-600, 10 % PEG 8000, 50 MM NH4COOH, 5MM MGCL2, 25 MM PHOSPHATE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal
*PLUS
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlConA1drop
22.75 mMM6M1drop
37 %Jeffamine M-6001reservoir
410 %PEG80001reservoir
550 mMammonium formate1reservoir
65 mM1reservoirMgCl2
725 mMphosphate1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 30, 1997 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / Num. obs: 71100 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 17
Reflection shellResolution: 2→2.1 Å / Redundancy: 7 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 6.3 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 498686
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.32

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ENQ

1enq


Resolution: 2→15 Å / Isotropic thermal model: RESTRAINED / Cross valid method: X-PLOR / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER, 1991
RfactorNum. reflection% reflection
Rfree0.211 6680 10 %
Rwork0.1752 --
all-67133 -
obs-67133 100 %
Displacement parametersBiso mean: 25 Å2
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7236 0 105 386 7727
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.657
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.276 -10 %
Rwork0.2344 786 -
obs--99.8 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg27.358
X-RAY DIFFRACTIONx_improper_angle_deg1.556
LS refinement shell
*PLUS
Highest resolution: 2 Å / Rfactor Rfree: 0.276 / % reflection Rfree: 10 % / Rfactor obs: 0.234

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