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- PDB-1jyi: CONCANAVALIN A/12-MER PEPTIDE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1jyi
TitleCONCANAVALIN A/12-MER PEPTIDE COMPLEX
Components
  • 12-mer peptide
  • Concanavalin-Br
KeywordsSUGAR BINDING PROTEIN / LECTIN
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 domain / Legume lectin, beta chain, Mn/Ca-binding site / : / 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 domain / Legume lectin, beta chain, Mn/Ca-binding site / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCanavalia ensiformis (jack bean)
synthetic construct (others)
MethodX-RAY DIFFRACTION / Resolution: 2.75 Å
AuthorsJain, D. / Kaur, K.J. / Sundaravadivel, B. / Salunke, D.M.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Structural and Functional Consequences of Peptide-carbohydrate Mimicry. Crystal Structure of a Carbohydrate-mimicking Peptide Bound to Concanavalin A.
Authors: Jain, D. / Kaur, K.J. / Sundaravadivel, B. / Salunke, D.M.
History
DepositionSep 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 21, 2017Group: Advisory / Database references ...Advisory / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_nat / pdbx_distant_solvent_atoms / pdbx_entity_src_syn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_nat.pdbx_beg_seq_num ..._entity.pdbx_description / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Concanavalin-Br
B: Concanavalin-Br
C: Concanavalin-Br
D: Concanavalin-Br
P: 12-mer peptide
Q: 12-mer peptide
R: 12-mer peptide
S: 12-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,33116
Polymers107,9518
Non-polymers3808
Water5,206289
1
A: Concanavalin-Br
B: Concanavalin-Br
P: 12-mer peptide
Q: 12-mer peptide
hetero molecules

A: Concanavalin-Br
B: Concanavalin-Br
P: 12-mer peptide
Q: 12-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,33116
Polymers107,9518
Non-polymers3808
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
2
C: Concanavalin-Br
D: Concanavalin-Br
R: 12-mer peptide
S: 12-mer peptide
hetero molecules

C: Concanavalin-Br
D: Concanavalin-Br
R: 12-mer peptide
S: 12-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,33116
Polymers107,9518
Non-polymers3808
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)102.545, 118.323, 252.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Concanavalin-Br / Con Br / Concanavalin A


Mass: 25622.385 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P55915
#2: Protein/peptide
12-mer peptide


Mass: 1365.444 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. / Source: (synth.) synthetic construct (others)
#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.: 289 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 65.32 %
Crystal grow
*PLUS
pH: 9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.32 mMpeptide1drop
21 Mammonium sulfate1reservoir
350 mMTris1reservoirpH9.0

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.75→10 Å / Num. obs: 34767 / % possible obs: 86.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.67 / Net I/σ(I): 6
Reflection shellResolution: 2.75→10 Å
Reflection
*PLUS
Redundancy: 3 % / Num. measured all: 47255 / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
Lowest resolution: 3.07 Å / % possible obs: 67.5 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementStarting model: 5CNA

5cna


Resolution: 2.75→10 Å / σ(F): 0 /
RfactorNum. reflection
Rfree0.265 -
Rwork0.192 -
obs-34767
Refinement stepCycle: LAST / Resolution: 2.75→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7628 0 8 289 7925
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.632

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