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- PDB-2ctv: HIGH RESOLUTION CRYSTALLOGRAPHIC STUDIES OF NATIVE CONCANAVALIN A... -

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Basic information

Entry
Database: PDB / ID: 2ctv
TitleHIGH RESOLUTION CRYSTALLOGRAPHIC STUDIES OF NATIVE CONCANAVALIN A USING RAPID LAUE DATA COLLECTION METHODS AND THE INTRODUCTION OF A MONOCHROMATIC LARGE-ANGLE OSCILLATION TECHNIQUE (LOT)
ComponentsCONCANAVALIN A
KeywordsLECTIN
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: 1.95 Å
AuthorsWeisgerber, S. / Helliwell, J.R.
Citation
Journal: J.Chem.Soc.,Faraday Trans. / Year: 1993
Title: High Resolution Crystallographic Studies of Native Concanavalin a Using Rapid Laue Data Collection Methods and the Introduction of a Monochromatic Large-Angle Oscillation Technique (Lot)
Authors: Weisgerber, S. / Helliwell, J.R.
#1: Journal: Embo J. / Year: 1992
Title: Non-Glycosylated Recombinant Pro-Concanavalin a is Active without Polypeptide Cleavage
Authors: Min, W. / Dunn, A.J. / Jones, D.H.
History
DepositionAug 10, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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

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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)25,7173
Polymers25,6221
Non-polymers952
Water2,630146
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)102,87012
Polymers102,4904
Non-polymers3808
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area10270 Å2
ΔGint-114 kcal/mol
Surface area32360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)88.700, 86.500, 62.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: ALA A 207 - ASP A 208 OMEGA ANGLE = 2.134 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Components on special symmetry positions
IDModelComponents
11A-385-

HOH

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Components

#1: Protein CONCANAVALIN A


Mass: 25622.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canavalia ensiformis (jack bean) / Organ: BEAN / References: UniProt: P02866
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.34 Å3/Da / Density % sol: 47.4 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.95→8 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.153 -
obs0.153 15442
Refinement stepCycle: LAST / Resolution: 1.95→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 2 146 1957
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg2.97
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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