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- PDB-2enr: CO-CRYSTALS OF DEMETALLIZED CONCANAVALIN A WITH CADMIUM HAVING A ... -

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Basic information

Entry
Database: PDB / ID: 2enr
TitleCO-CRYSTALS OF DEMETALLIZED CONCANAVALIN A WITH CADMIUM HAVING A CADMIUM ION BOUND IN BOTH THE S1 SITE AND THE S2 SITE
ComponentsCONCANAVALIN A
KeywordsLECTIN / CONCANAVALIN A / PLANT LECTIN / CARBOHYDRATE BINDING / METAL BINDING / CADMIUM
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
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBouckaert, J. / Loris, R. / Wyns, L.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Zinc/calcium- and cadmium/cadmium-substituted concanavalin A: interplay of metal binding, pH and molecular packing.
Authors: Bouckaert, J. / Loris, R. / Wyns, L.
#1: Journal: Lectins: Biol.Biochem.Clin.Biochem. / Year: 1996
Title: Changes in Crystal Space Group and Multimeric Structure of Concanavalin a as a Function of Metal Ion Binding and Ph
Authors: Bouckaert, J. / Loris, R. / Wyns, L.
History
DepositionJul 14, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: 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: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CONCANAVALIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8473
Polymers25,6221
Non-polymers2252
Water1,78399
1
A: CONCANAVALIN A
hetero molecules

A: CONCANAVALIN A
hetero molecules

A: CONCANAVALIN A
hetero molecules

A: CONCANAVALIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,38912
Polymers102,4904
Non-polymers8998
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_564x,-y+1,-z-11
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)63.200, 87.690, 89.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-341-

HOH

DetailsTHE ASYMMETRIC UNIT CONTAINS A MONOMER OF 237 AMINO ACIDS. THE BIOLOGICALLY ACTIVE UNIT IS A CANONICAL DIMER (BELOW PH 6) OR TETRAMER. THE FOLLOWING SURFACE LOOPS ARE IN WEAK ELECTRON DENSITY: 118-123 AND 160-163. A CD2+ IS SUBSTITUTED FOR MN2+ IN THE TRANSITION METAL ION SITE S1. A CD2+ IS SUBSTITUTED FOR CA2+ IN THE CALCIUM SITE S2.

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Components

#1: Protein CONCANAVALIN A / CON A


Mass: 25622.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CADMIUM/CADMIUM COMPLEX / Source: (natural) Canavalia ensiformis (jack bean) / Organ: BEAN / References: UniProt: P02866
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 39.8 %
Crystal growpH: 5 / Details: pH 5.0
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
111 mg/mlprotein1drop
22 Mammonium sulfate1reservoir
3100 mMsodium acetate1reservoir
45 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jun 13, 1993 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.38→11 Å / Num. obs: 30650 / % possible obs: 96.02 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 33.7 Å2 / Rsym value: 0.054 / Net I/σ(I): 11.2
Reflection shellResolution: 2.38→2.45 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.299 / % possible all: 80.9
Reflection
*PLUS
Highest resolution: 2.35 Å / Lowest resolution: 10 Å / Num. obs: 10111 / % possible obs: 95.3 % / Num. measured all: 30650 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
Highest resolution: 2.35 Å / Lowest resolution: 2.46 Å / % possible obs: 75.1 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 10.7

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESSdata reduction
CCP4(ROTAVATA)data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CON

1con


Resolution: 2.35→10 Å / Isotropic thermal model: RESTRAINED / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.1731 --
obs0.1731 10111 96.02 %
Displacement parametersBiso mean: 16 Å2
Refinement stepCycle: LAST / Resolution: 2.35→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 2 99 1910
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg3.069
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.08
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.465
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
LS refinement shellResolution: 2.3→2.42 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.262 560 -
obs--35 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.08
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.465
LS refinement shell
*PLUS
Rfactor obs: 0.262

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