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- PDB-1joj: CONCANAVALIN A-HEXAPEPTIDE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1joj
TitleCONCANAVALIN A-HEXAPEPTIDE COMPLEX
Components
  • Concanavalin-Br
  • HEXAPEPTIDE
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, 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsJain, D. / Kaur, K. / Salunke, D.M.
Citation
Journal: Biochemistry / Year: 2001
Title: Enhanced binding of a rationally designed peptide ligand of concanavalin a arises from improved geometrical complementarity.
Authors: Jain, D. / Kaur, K.J. / Salunke, D.M.
#1: Journal: Biophys.J. / Year: 2001
Title: Plasticity in Protein-Peptide Recognition: Crystal Structures of Two Different Peptides Bound to Concanavalin A
Authors: Jain, D. / Kaur, K.J. / Salunke, D.M.
#2: Journal: 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
DepositionJul 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2001Provider: 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: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_nat / 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 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Aug 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.pdbx_leaving_atom_flag / _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: HEXAPEPTIDE
Q: HEXAPEPTIDE
R: HEXAPEPTIDE
S: HEXAPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,65416
Polymers106,2748
Non-polymers3808
Water3,549197
1
A: Concanavalin-Br
B: Concanavalin-Br
P: HEXAPEPTIDE
Q: HEXAPEPTIDE
hetero molecules

A: Concanavalin-Br
B: Concanavalin-Br
P: HEXAPEPTIDE
Q: HEXAPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,65416
Polymers106,2748
Non-polymers3808
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
2
C: Concanavalin-Br
D: Concanavalin-Br
R: HEXAPEPTIDE
S: HEXAPEPTIDE
hetero molecules

C: Concanavalin-Br
D: Concanavalin-Br
R: HEXAPEPTIDE
S: HEXAPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,65416
Polymers106,2748
Non-polymers3808
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)102.685, 118.384, 253.593
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
HEXAPEPTIDE


Mass: 946.103 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.: 197 / 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: 3.62 Å3/Da / Density % sol: 66.06 %
Crystal grow
*PLUS
pH: 9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.32 mMprotein1drop
450 mMTris1reservoir
2peptide1drop20-fold molar excess
3ammonium sulfate1reservoirpH9.0

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178
DetectorDetector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionHighest resolution: 3 Å / Num. obs: 23957 / % possible obs: 78.1 % / Redundancy: 3 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 10.6
Reflection shellResolution: 3→3.13 Å / % possible obs: 71.8 % / Mean I/σ(I) obs: 5.37 / % possible all: 71.8
Reflection shell
*PLUS
Rmerge(I) obs: 0.257

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNS0.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CNA

5cna


Resolution: 3→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1117 4.8 %RANDOM
Rwork0.186 ---
all-23160 --
obs-23160 78.1 %-
Displacement parametersBiso mean: 28.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7512 0 8 197 7717
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.24
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.671.5
X-RAY DIFFRACTIONc_mcangle_it8.72
X-RAY DIFFRACTIONc_scbond_it82
X-RAY DIFFRACTIONc_scangle_it11.452.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4CIS.INP
X-RAY DIFFRACTION5ACE.PAR
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.8 % / Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.24
X-RAY DIFFRACTIONc_mcbond_it5.671.5
X-RAY DIFFRACTIONc_scbond_it82
X-RAY DIFFRACTIONc_mcangle_it8.72
X-RAY DIFFRACTIONc_scangle_it11.452.5

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