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- PDB-2dh1: Crystal structure of peanut lectin lactose-azobenzene-4,4'-dicarb... -

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Basic information

Entry
Database: PDB / ID: 2dh1
TitleCrystal structure of peanut lectin lactose-azobenzene-4,4'-dicarboxylic acid-lactose complex
ComponentsGalactose-binding lectin
KeywordsSUGAR BINDING PROTEIN / LEGUME LECTIN / AGGLUTININ / CROSSLINK / OPEN QUATERNARY STRUCTURE / CARBOHYDRATE SPECIFICITY / MULTIVALENCY
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 / : / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Galactose-binding lectin
Similarity search - Component
Biological speciesArachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 7.65 Å
AuthorsNatchiar, S.K. / Srinivas, O. / Nivedita, M. / Sagarika, D. / Jayaraman, N. / Surolia, A. / Vijayan, M.
Citation
Journal: Curr.Sci. / Year: 2006
Title: Multivalency in lectins - A crystallographic, modelling and light-scattering study involving peanut lectin and a bivalent ligand
Authors: Natchiar, S.K. / Srinivas, O. / Nivedita, M. / Sagarika, D. / Jayaraman, N. / Surolia, A. / Vijayan, M.
#1: 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.
#2: 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.
#3: 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.
#4: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004
Title: Structural plasticity of peanut lectin: an X-ray analysis involving variation in pH, ligand binding and crystal structure
Authors: Natchiar, S.K. / Jeyaprakash, A.A. / Ramya, T.N. / Thomas, C.J. / Suguna, K. / Surolia, A. / Vijayan, M.
#5: Journal: J.Am.Chem.Soc. / Year: 2002
Title: Photoswitchable multivalent sugar ligands: synthesis, isomerization, and lectin binding studies of azobenzene-glycopyranoside derivatives
Authors: Srinivas, O. / Mitra, N. / Surolia, A. / Jayaraman, N.
History
DepositionMar 17, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galactose-binding lectin
B: Galactose-binding lectin
C: Galactose-binding lectin
D: Galactose-binding lectin


Theoretical massNumber of molelcules
Total (without water)100,8364
Polymers100,8364
Non-polymers00
Water00
1
A: Galactose-binding lectin
D: Galactose-binding lectin


Theoretical massNumber of molelcules
Total (without water)50,4182
Polymers50,4182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galactose-binding lectin
C: Galactose-binding lectin


Theoretical massNumber of molelcules
Total (without water)50,4182
Polymers50,4182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.750, 92.750, 473.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
DetailsBiological molecule is a tetramer. It can be generated from the dimer in the asymmetric by symmetry

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Components

#1: Protein
Galactose-binding lectin / Agglutinin / PNA / Coordinate model: Cα atoms only


Mass: 25208.955 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Arachis hypogaea (peanut) / References: UniProt: P02872

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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: 4.6 Å3/Da / Density % sol: 73.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12% PEG 8000, 0.05M sodium phosphate, 0.2M sodium cholride, 0.02% sodium azide, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 3, 2003 / Details: OSMIC MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 7.65→20 Å / Num. obs: 2273 / % possible obs: 99.8 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1
Reflection shellResolution: 7.65→7.8 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.6 / Num. unique all: 219 / Rsym value: 0.524 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PEL

2pel


Resolution: 7.65→20 Å / Cor.coef. Fo:Fc: 0.812 / Cor.coef. Fo:Fc free: 0.836 / SU B: 897.888 / SU ML: 6.067 / ESU R: 4.956 / ESU R Free: 5.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: RIGID BODY REFINEMENT. THE COORDINATES FOR ONLY THE ALPHA CARBONS ARE PRESENT IN THE STRUCTURE. THE NUMBER OF MISSING ATOMS WAS SO MUCH THAT REMARK 470 FOR THE MISSING ATOMS LIST WERE REMOVED.
RfactorNum. reflection% reflectionSelection details
Rfree0.3772 106 4.7 %RANDOM
Rwork0.35458 ---
obs0.35562 2165 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 7.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms928 0 0 0 928
LS refinement shellResolution: 7.65→7.91 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 --
Rwork0.355 142 -
obs--100 %

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