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- PDB-1cjp: CONCANAVALIN A COMPLEX WITH 4'-METHYLUMBELLIFERYL-ALPHA-D-GLUCOPY... -

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Basic information

Entry
Database: PDB / ID: 1cjp
TitleCONCANAVALIN A COMPLEX WITH 4'-METHYLUMBELLIFERYL-ALPHA-D-GLUCOPYRANOSIDE
ComponentsCONCANAVALIN A
KeywordsLECTIN / LEGUME LECTIN
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 domain / Legume lectin, beta chain, Mn/Ca-binding site / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily ...Legume lectin / 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
: / 4-METHYLUMBELLIFERYL-ALPHA-D-GLUCOSE / Concanavalin-A
Similarity search - Component
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsHamodrakas, S.J. / Kanellopoulos, P.N. / Tucker, P.A.
Citation
Journal: J.Struct.Biol. / Year: 1997
Title: The crystal structure of the complex of concanavalin A with 4'-methylumbelliferyl-alpha-D-glucopyranoside.
Authors: Hamodrakas, S.J. / Kanellopoulos, P.N. / Pavlou, K. / Tucker, P.A.
#1: Journal: J.Struct.Biol. / Year: 1996
Title: A Triclinic Crystal Form of the Lectin Concanavalin A
Authors: Kanellopoulos, P.N. / Tucker, P.A. / Pavlou, K. / Agianian, B. / Hamodrakas, S.J.
#2: Journal: J.Struct.Biol. / Year: 1996
Title: The Crystal Structure of the Complexes of Concanavalin a with 4'-Nitrophenyl-Alpha-D-Mannopyranoside and 4'-Nitrophenyl-Alpha-D-Glucopyranoside
Authors: Kanellopoulos, P.N. / Pavlou, K. / Perrakis, A. / Agianian, B. / Vorgias, C.E. / Mavrommatis, C. / Soufi, M. / Tucker, P.A. / Hamodrakas, S.J.
History
DepositionOct 3, 1996Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 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
C: CONCANAVALIN A
D: CONCANAVALIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,22316
Polymers102,4904
Non-polymers1,73312
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11480 Å2
ΔGint-109 kcal/mol
Surface area32770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.620, 128.710, 82.230
Angle α, β, γ (deg.)90.00, 118.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
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: P02866
#2: Sugar
ChemComp-MUG / 4-METHYLUMBELLIFERYL-ALPHA-D-GLUCOSE


Type: D-saccharide / Mass: 338.309 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C16H18O8
#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.: 162 / 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: 3.7 Å3/Da / Density % sol: 66.78 %
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
170 mg/mlprotein1drop
210 mMTris1reservoir
31 Mammonium sulfate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 30, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 37358 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.074
Reflection
*PLUS
Highest resolution: 2.78 Å / Lowest resolution: 48 Å / Num. measured all: 151116
Reflection shell
*PLUS
Highest resolution: 2.78 Å / Lowest resolution: 2.9 Å / % possible obs: 95.2 % / Rmerge(I) obs: 0.238

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VAM

1vam


Resolution: 2.78→8 Å / σ(F): 0
RfactorNum. reflection
Rfree0.216 -
Rwork0.182 -
obs0.182 35273
Displacement parametersBiso mean: 51.41 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.78→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7236 0 104 162 7502
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.9
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

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