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- PDB-1gic: CONCANAVALIN A COMPLEXED WITH METHYL ALPHA-D-GLUCOPYRANOSIDE -

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Basic information

Entry
Database: PDB / ID: 1gic
TitleCONCANAVALIN A COMPLEXED WITH METHYL ALPHA-D-GLUCOPYRANOSIDE
ComponentsCONCANAVALIN A
KeywordsLECTIN / COMPLEX / SACCHARIDE
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
methyl alpha-D-glucopyranoside / : / Concanavalin-A
Similarity search - Component
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR, molecular replacement / Resolution: 2 Å
AuthorsBradbrook, G.M. / Gleichmann, T. / Harrop, S.J. / Helliwell, J.R. / Habash, J. / Kalb(Gilboa), A.J. / Tong, L. / Wan, T.C.M. / Yariv, J.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structure solution of a cubic crystal of concanavalin A complexed with methyl alpha-D-glucopyranoside.
Authors: Harrop, S.J. / Helliwell, J.R. / Wan, T.C. / Kalb, A.J. / Tong, L. / Yariv, J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Structure Solution of a Cubic Crystal of Concanavalin a Complexed with Methyl-Alpha-D-Glucopyranoside
Authors: Harrop, S.J. / Helliwell, J.R. / Wan, T.C.M. / Kalb(Gilboa), A.J. / Tong, L. / Yariv, J.
History
DepositionAug 8, 1996Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / software / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _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.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 / _software.name / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 9, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8238
Polymers51,2452
Non-polymers5786
Water6,485360
1
A: CONCANAVALIN A
B: CONCANAVALIN A
hetero molecules

A: CONCANAVALIN A
B: CONCANAVALIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,64616
Polymers102,4904
Non-polymers1,15712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_556-x+1/2,y,-z+11
Buried area11030 Å2
ΔGint-110 kcal/mol
Surface area32800 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)167.800, 167.800, 167.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein CONCANAVALIN A


Mass: 25622.385 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P02866
#2: Sugar ChemComp-GYP / methyl alpha-D-glucopyranoside / METHYL-ALPHA-D-GLUCOPYRANOSIDE / ALPHA-METHYL-D-GLUCOPYRANOSIDE / methyl alpha-D-glucoside / methyl D-glucoside / methyl glucoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
IdentifierTypeProgram
DGlcp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-glucopyranoseCOMMON NAMEGMML 1.0
methyl-a-D-glucopyranosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68.5 %
Crystal growMethod: dialysis / pH: 6.8
Details: DIALYSIS; 5MM PROTEIN CONCENTRATION WITH, pH 6.8, dialysis

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: 1988 / Details: MIRROR AND MONOCHROMATOR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 34648 / % possible obs: 64 % / Redundancy: 30 % / Rmerge(I) obs: 0.046

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
XENGEN(TO 5.2A)data reduction
MOSFLM(TO 3A/2A)data reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MIR, molecular replacement
Starting model: PDB ENTRY 1CON

1con


Resolution: 2→100 Å
RfactorNum. reflection% reflection
Rwork0.17 --
obs0.17 34648 64 %
Refinement stepCycle: LAST / Resolution: 2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3618 0 30 360 4008
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg3.2
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_d2
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

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