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- PDB-1ces: CRYSTALS OF DEMETALLIZED CONCANAVALIN A SOAKED WITH ZINC HAVE A Z... -

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Basic information

Entry
Database: PDB / ID: 1ces
TitleCRYSTALS OF DEMETALLIZED CONCANAVALIN A SOAKED WITH ZINC HAVE A ZINC ION BOUND IN THE S1 SITE
ComponentsCONCANAVALIN A
KeywordsLECTIN / CONCANAVALIN A / ZINC / CONFORMATION
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 ...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 / MOLECULAR REPLACEMENT / Resolution: 2.7 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 A Resolution
Authors: Bouckaert, J. / Loris, R. / Poortmans, F. / Wyns, L.
History
DepositionFeb 15, 1996Processing site: BNL
Revision 1.0Feb 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Aug 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
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. CONCANAVALIN A EXISTS AS A TETRAMER ALTHOUGH THE ASYMMETRIC UNIT CONTAINS A DIMER. THE TETRAMER CAN BE GENERATED BY SYMMETRY OPERATORS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CONCANAVALIN A
B: CONCANAVALIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3764
Polymers51,2452
Non-polymers1312
Water70339
1
A: CONCANAVALIN A
B: CONCANAVALIN A
hetero molecules

A: CONCANAVALIN A
B: CONCANAVALIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,7518
Polymers102,4904
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)61.310, 86.200, 91.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein CONCANAVALIN A / CON A


Mass: 25622.385 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THERE ARE TWO MONOMERS (MR 25500 EACH) WITH IDENTICAL SEQUENCE
Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P02866
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsZINC ION IS PARTIALLY BOUND IN THE S1 SITE.

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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: 2.35 Å3/Da / Density % sol: 45.9 %
Crystal growpH: 5 / Details: pH 5.
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15.5 mg/mlprotein1drop
21 Mammonium sulfate1drop
350 mMsodium acetate1drop
42.5 %PEG60001drop
52 Mammonium sulfate1reservoir
6100 mMsodium acetate1reservoir
75 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jun 9, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→10 Å / Num. obs: 12557 / % possible obs: 91.5 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.085
Reflection
*PLUS
Num. measured all: 29303

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Processing

Software
NameClassification
X-PLORrefinement
MADNESdata reduction
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DEMETALLIZED CONCANAVALIN A (PDB ENTRY 1APN)

1apn


Resolution: 2.7→10 Å / Cross valid method: BRUNGER / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.249 -10 %RANDOM
Rwork0.204 ---
obs0.204 12557 91.5 %-
Displacement parametersBiso mean: 24.89 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3409 0 2 38 3449
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_deg2.4
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg27.8
X-RAY DIFFRACTIONx_improper_angle_deg1.78

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