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- PDB-1nls: CONCANAVALIN A AND ITS BOUND SOLVENT AT 0.94A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1nls
TitleCONCANAVALIN A AND ITS BOUND SOLVENT AT 0.94A RESOLUTION
ComponentsCONCANAVALIN A
KeywordsAGGLUTININ / CONCANAVALIN A / 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, 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 / SYNCHROTRON / Resolution: 0.94 Å
AuthorsDeacon, A.M. / Gleichmann, T. / Helliwell, J.R. / Kalb(Gilboa), A.J.
Citation
Journal: J.Chem.Soc.,Faraday Trans. / Year: 1997
Title: The Structure of Concanavalin a and its Bound Solvent Determined with Small-Molecule Accuracy at 0.94 A Resolution
Authors: Deacon, A. / Gleichmann, T. / Kalb(Gilboa), A.J. / Price, H. / Raftery, J. / Bradbrook, G. / Yariv, J. / Helliwell, J.R.
#1: Journal: J.Chem.Soc.,Faraday Trans. / Year: 1997
Title: Neutron Laue Diffraction Study of Concanavalin A. The Proton of Asp28
Authors: Habash, J. / Raftery, J. / Weisgerber, S. / Cassetta, A. / Lehmann, M.S. / Hoghoj, P. / Wilkinson, C. / Campbell, J.W. / Helliwell, J.R.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: High-Resolution Structures of Single-Metal-Substituted Concanavalin A: The Co,Ca-Protein at 1.6 A and the Ni,Ca-Protein at 2.0 A
Authors: Emmerich, C. / Helliwell, J.R. / Redshaw, M. / Naismith, J.H. / Harrop, S.J. / Raftery, J. / Kalb(Gilboa), A.J. / Yariv, J. / Dauter, Z. / Wilson, K.S.
#3: 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.
History
DepositionJan 28, 1997Processing site: BNL
Revision 1.0Nov 26, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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

Downloads & links

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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
Water5,747319
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 operation3_655-x+1,y,-z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)89.550, 86.460, 62.110
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-534-

HOH

21A-544-

HOH

DetailsCONCANAVALIN A EXISTS AS A TETRAMER, ALTHOUGH THE ASYMMETRIC UNIT CONTAINS A MONOMER. THE TETRAMER CAN BE GENERATED BY SYMMETRY OPERATORS.

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Components

#1: Protein CONCANAVALIN A


Mass: 25622.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack 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.: 319 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49 %
Crystal growpH: 6.8 / Details: pH 6.8

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.92
DetectorDetector: CCD / Date: 1994 / Details: MIRROR + MONO POINT FOCUSSING
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionNum. obs: 116923 / % possible obs: 75.4 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.093
Reflection shellResolution: 0.94→1.01 Å / Rmerge(I) obs: 0.15 / % possible all: 30.4

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Processing

Software
NameClassification
SHELXL-97model building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing
RefinementResolution: 0.94→8 Å / Num. parameters: 19158 / Num. restraintsaints: 23649
Stereochemistry target values: 0.02A BOND LENGTH ESDS RESTRAINT
Details: RESIDUE THR 120 IS POORLY DEFINED IN ELECTRON DENSITY. THE FOLLOWING RESIDUES HAVE SIDE CHAINS MODELLED WITH TWO CONFORMATIONS AND WERE REFINED WITH COMPLEMENTARY OCCUPANCIES: LEU 9, SER 21, ...Details: RESIDUE THR 120 IS POORLY DEFINED IN ELECTRON DENSITY. THE FOLLOWING RESIDUES HAVE SIDE CHAINS MODELLED WITH TWO CONFORMATIONS AND WERE REFINED WITH COMPLEMENTARY OCCUPANCIES: LEU 9, SER 21, ILE 25, ILE 27, LYS 39, MET 42, LYS 59, ARG 60, VAL 65, SER 72, ASP 78, LEU 107, SER 110, SER 113, ASN 124, SER 164, SER 185, VAL 188, GLU 192, THR 196, SER 204, SER 215, ASP 218, SER 220, SER 223. CIS PEPTIDES 1 AND 2 ARE DUE TO POORLY DEFINED ELECTRON DENSITY.
RfactorNum. reflection% reflection
Rfree0.154 1167 1 %
obs0.127 -75 %
all-116712 -
Solvent computationSolvent model: SHELXL SWAT
Refine analyzeLuzzati coordinate error obs: 0.06 Å / Luzzati sigma a obs: 0.02 Å
Refinement stepCycle: LAST / Resolution: 0.94→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 2 323 2134

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