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- PDB-1enq: CO-CRYSTALS OF DEMETALLIZED CONCANAVALIN A WITH ZINC HAVING A ZIN... -

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Basic information

Entry
Database: PDB / ID: 1enq
TitleCO-CRYSTALS OF DEMETALLIZED CONCANAVALIN A WITH ZINC HAVING A ZINC ION BOUND IN THE S1 SITE
ComponentsCONCANAVALIN A
KeywordsPLANT LECTIN (AGGLUTININ) / CONCANAVALIN A / ZINC / PLANT LECTIN / AGGLUTININ
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
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsBouckaert, J. / Loris, R. / Poortmans, F. / Wyns, L.
Citation
Journal: J.Biol.Chem. / Year: 1996
Title: Sequential structural changes upon zinc and calcium binding to metal-free concanavalin A.
Authors: Bouckaert, J. / Poortmans, F. / Wyns, L. / Loris, R.
#1: Journal: Proteins / Year: 1995
Title: Crystallographic Structure of Metal-Free Concanavalin a at 2.5 Angstrom Resolution
Authors: Bouckaert, J. / Loris, R. / Poortmans, F. / Wyns, L.
History
DepositionMar 20, 1996Processing site: BNL
Revision 1.0Aug 17, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Advisory / Data collection / Other
Category: diffrn_detector / pdbx_database_status ...diffrn_detector / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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 / _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
Remark 700SHEET THE MOST STRIKING FEATURE OF CONCANAVALIN A IS TWO LARGE BETA SHEETS IN THE STRUCTURE ...SHEET THE MOST STRIKING FEATURE OF CONCANAVALIN A IS TWO LARGE BETA SHEETS IN THE STRUCTURE COMPRISING 119 OF THE 237 AMINO ACIDS. THERE IS NO ALPHA HELIX. THE REMAINING AMINO ACIDS FORM A SERIES OF LOOPS AND TURNS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)102,7518
Polymers102,4904
Non-polymers2624
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-188 kcal/mol
Surface area32700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.230, 113.030, 122.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE ASYMMETRIC UNIT CONTAINS FOUR MONOMERS EACH CONTAINING 237 AMINO ACIDS (CHAINS A, B, C, AND D), FORMING A BIOLOGICALLY FUNCTIONAL TETRAMER. THE FOLLOWING RESIDUES ARE IN VERY WEAK DENSITY IN ALL FOUR MONOMERS: 99 - 101, 117 - 122, 160 - 167, 204 - 204, 235 - 237. THE SURFACE LOOP RESIDUES 14 - 19 ARE IN WEAK DENSITY IN CHAIN B, ARE BADLY DEFINED BY THE ELECTRON DENSITY IN CHAIN C, AND UNDEFINED IN CHAIN D. THE ATOMS WERE MODELLED AS OXT OF THE PREVIOUS RESIDUE. NO DENSITY IS OBSERVED FOR THE REST OF THE RESIDUE. PDB CHOSE REPRESENT THESE ATOMS AS THE N ATOM OF THE PROCEEDING RESIDU N SER A 161 N SER B 160 N SER C 160 N THR D 15 N SER D 160

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Components

#1: Protein
CONCANAVALIN A / CON A


Mass: 25622.385 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: ZINC COMPLEX / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P02866
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.26 Å3/Da / Density % sol: 47.4 %
Crystal growpH: 5 / Details: pH 5.
Crystal
*PLUS
Density % sol: 43.7 %
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 M1reservoir(NH4)2SO4
260 mMsodium acetate1reservoir
33 %PEG50001reservoir
41.73 mg/mlmetal-free ConA1drop
510 mM1dropZnCl2
62 M1reservoir(NH4)2SO4
760 mMsodium acetate1reservoir
83 %PEG50001reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jan 30, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.19→42 Å / Num. obs: 32457 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.011
Reflection
*PLUS
Highest resolution: 2.49 Å / Lowest resolution: 15 Å / Num. obs: 31981 / % possible obs: 97.5 % / Num. measured all: 121921 / Rmerge(I) obs: 0.0112

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementResolution: 2.5→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.284 -10 %
Rwork0.198 --
obs0.198 31981 97.5 %
Displacement parametersBiso mean: 42.69 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7036 0 2 249 7287
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.029
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_deg2.69
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.03
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.35
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.1978 / Rfactor Rfree: 0.2841 / Rfactor Rwork: 0.1978
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.687
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.034
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.346

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