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- PDB-1cq9: PEANUT LECTIN-TRICLINIC FORM -

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Basic information

Entry
Database: PDB / ID: 1cq9
TitlePEANUT LECTIN-TRICLINIC FORM
ComponentsPROTEIN (PEANUT LECTIN)
KeywordsLECTIN / LEGUME LECTIN / OPEN QUATERNARY STRUCTURE / TRICLINIC FORM / ACIDIC PH
Function / homology
Function and homology information


carbohydrate binding / 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
: / Galactose-binding lectin
Similarity search - Component
Biological speciesArachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsRavishankar, R. / Suguna, K. / Surolia, A. / Vijayan, M.
Citation
Journal: Proteins / Year: 2001
Title: Crystal structures of the peanut lectin-lactose complex at acidic pH: retention of unusual quaternary structure, empty and carbohydrate bound combining sites, molecular mimicry and crystal ...Title: Crystal structures of the peanut lectin-lactose complex at acidic pH: retention of unusual quaternary structure, empty and carbohydrate bound combining sites, molecular mimicry and crystal packing directed by interactions at the combining site.
Authors: Ravishankar, R. / Thomas, C.J. / Suguna, K. / Surolia, A. / Vijayan, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Structures of the Complexes of Peanut Lectin with Methyl-Beta-Galactose and N- Acetyllactosamine and a Comparative Study of Carbohydrate Binding in Gal/ Galnac-Specific Legume Lectins
Authors: Ravishankar, R. / Suguna, K. / Surolia, A. / Vijayan, M.
#2: Journal: Curr.Sci. / Year: 1997
Title: The Specificity of Peanut Agglutinin for Thomsen-Friedenreich Antigen is Mediated by Water-Bridges
Authors: Ravishankar, R. / Ravindran, M. / Suguna, K. / Surolia, A. / Vijayan, M.
#3: Journal: J.Mol.Biol. / Year: 1996
Title: Conformation, Protein-Carbohydrate Interactions and a Novel Subunit Association in the Refined Structure of Peanut Lectin-Lactose Complex
Authors: Banerjee, R. / Das, K. / Ravishankar, R. / Suguna, K. / Surolia, A. / Vijayan, M.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Crystal Structure of Peanut Lectin, a Protein with an Unusual Quaternary Structure
Authors: Banerjee, R. / Mande, S.C. / Ganesh, V. / Das, K. / Dhanaraj, V. / Mahanta, S.K. / Suguna, K. / Surolia, A. / Vijayan, M.
History
DepositionAug 6, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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: PROTEIN (PEANUT LECTIN)
B: PROTEIN (PEANUT LECTIN)
C: PROTEIN (PEANUT LECTIN)
D: PROTEIN (PEANUT LECTIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,21612
Polymers100,8364
Non-polymers3808
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.64, 71.79, 86.42
Angle α, β, γ (deg.)65.35, 77.66, 72.31
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
PROTEIN (PEANUT LECTIN) / PEANUT AGGLUTININ


Mass: 25208.955 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Arachis hypogaea (peanut) / References: UniProt: P02872
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn

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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: 2.84 Å3/Da / Density % sol: 56.72 %
Crystal growpH: 4.6 / Details: pH 4.6
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.4 / Method: microdialysis / Details: Salunke, D.M., (1983) FEBS Lett., 156, 127.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mg/mlprotein1drop
240 %(w/v)PEG60001drop
30.2 M1reservoirNaCl
40.05 Msodium acetate1reservoir
51.5 mMlactose1reservoir
6phosphate1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→28.7 Å / Num. obs: 18342 / % possible obs: 82.32 % / Redundancy: 1.39 % / Rmerge(I) obs: 0.1572 / Net I/σ(I): 2.53
Reflection
*PLUS
Highest resolution: 3.5 Å / Num. obs: 11935 / % possible obs: 84.3 % / Num. measured all: 16538 / Rmerge(I) obs: 0.157
Reflection shell
*PLUS
% possible obs: 81.4 % / Rmerge(I) obs: 0.301

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
XDSdata reduction
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PEL WITHOUT SUGAR AND WATER

2pel


Resolution: 3.5→10 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
Details: THERE IS A TETRAMER IN THE UNIT CELL WITHOUT 222 OR FOUR-FOLD SYMMETRY.
RfactorNum. reflection% reflectionSelection details
Rfree0.278 583 10.1 %RANDOM
Rwork0.217 ---
obs0.217 5778 43.1 %-
Displacement parametersBiso mean: 20.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.37 Å
Luzzati d res low-10 Å
Refinement stepCycle: LAST / Resolution: 3.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6972 0 8 0 6980
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.021
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_deg2.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.95
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
Refine LS restraints NCSNCS model details: RESTRAIN
LS refinement shellResolution: 3.5→3.71 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 49 9.4 %
Rwork0.237 470 -
obs--23.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2WAT.PARWAT.TOP
X-RAY DIFFRACTION3PARAM1.CHOTOPH1.CHO
Refinement
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 10 Å / Rfactor obs: 0.217 / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.95
LS refinement shell
*PLUS
Rfactor Rfree: 0.276 / Rfactor Rwork: 0.237

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