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- PDB-1qdo: MAN(APLHA1-3)MAN(ALPHA1-O)METHYL CONCANAVALIN A COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1qdo
TitleMAN(APLHA1-3)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 ...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
: / Concanavalin-Br / Concanavalin-Br
Similarity search - Component
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 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
DepositionMay 24, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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.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 / _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
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)104,29516
Polymers102,4904
Non-polymers1,80512
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12180 Å2
ΔGint-79 kcal/mol
Surface area33380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.410, 64.530, 126.960
Angle α, β, γ (deg.)90.00, 93.21, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
DetailsTHE ASYMMETRIC UNIT CONTAINS A TETRAMER, COMPOSED OF IDENTICAL MONOMERS OF 237 AMINO ACIDS. THE FOLLOWING RESIDUES ARE IN WEAK ELECTRON DENSITY: FROM 118 TO 121 AND 205.

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Components

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


Mass: 25622.385 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: CANAVALIA ENSIFORMIS BEANS / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: CONA_CANBR, UniProt: P55915*PLUS
#2: Polysaccharide
alpha-D-mannopyranose-(1-3)-methyl alpha-D-mannopyranoside


Type: oligosaccharide / Mass: 356.323 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManp[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/a3-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2

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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: 8
Details: DROP: 5 MICROLITER 5 MG/ML CON A, 5 MM SUGAR + 5 MICROLITER 14% PEG 8000, 35 MM POTASSIUM PHOSPHATE; 500 MICROLITER BOTTOM SOLUTION, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal
*PLUS
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlConA1drop
25 mMM3M1drop
314 %PEG80001reservoir
435 mMpotassium phosphate1reservoir

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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: Feb 10, 1999 / 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: 2.8→25 Å / Num. obs: 24411 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 28.85 Å2 / Rmerge(I) obs: 0.168 / Net I/σ(I): 17.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 8 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 3.9 / Num. unique all: 2420 / % possible all: 100
Reflection
*PLUS
Num. measured all: 195361
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

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

1enq


Resolution: 2.8→25 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber, 1991 / Details: NCS restraints grouped B-factor refinement
RfactorNum. reflection% reflection
Rfree0.257 2169 10 %
Rwork0.164 --
obs-24262 99.9 %
Displacement parametersBiso mean: 33 Å2
Refinement stepCycle: LAST / Resolution: 2.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7236 0 104 33 7373
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg1.826
X-RAY DIFFRACTIONx_dihedral_angle_d27.393
X-RAY DIFFRACTIONx_improper_angle_d1.699
Refine LS restraints NCSNCS model details: RESTRAINTS WEIGHT-NCS=602 SIGB=2.5 / Rms dev Biso : 2.5 Å2
LS refinement shellResolution: 2.8→2.93 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.416 -10 %
Rwork0.268 2701 -
obs--100 %
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: 2.8 Å / Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.164
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.393
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.699
LS refinement shell
*PLUS
Rfactor Rfree: 0.416 / % reflection Rfree: 10 % / Rfactor Rwork: 0.268 / Rfactor obs: 0.268

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