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- PDB-1v6m: Peanut Lectin with 9mer peptide (IWSSAGNVA) -

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Basic information

Entry
Database: PDB / ID: 1v6m
TitlePeanut Lectin with 9mer peptide (IWSSAGNVA)
ComponentsGalactose-binding lectin
KeywordsSUGAR BINDING PROTEIN / Lectin / agglutinin / open quaternary association and monoclinic
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 / Isomorphous replacement / Resolution: 2.7 Å
AuthorsKundhavai Natchiar, S. / Arockia Jeyaprakash, A. / Ramya, T.N.C. / Thomas, C.J. / Suguna, K. / Surolia, A. / Vijayan, M.
Citation
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: Kundhavai Natchiar, S. / Arockia Jeyaprakash, A. / Ramya, T.N. / Thomas, C.J. / Suguna, K. / Surolia, A. / Vijayan, M.
#1: Journal: PROTEINS: STRUCT.,FUNCT.,GENET. / 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.
History
DepositionDec 2, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_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_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_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_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: Galactose-binding lectin
B: Galactose-binding lectin
C: Galactose-binding lectin
D: Galactose-binding lectin
E: Galactose-binding lectin
F: Galactose-binding lectin
G: Galactose-binding lectin
H: Galactose-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,41124
Polymers197,6518
Non-polymers76016
Water6,485360
1
A: Galactose-binding lectin
B: Galactose-binding lectin
C: Galactose-binding lectin
D: Galactose-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,20612
Polymers98,8264
Non-polymers3808
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Galactose-binding lectin
F: Galactose-binding lectin
G: Galactose-binding lectin
H: Galactose-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,20612
Polymers98,8264
Non-polymers3808
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.852, 126.139, 84.825
Angle α, β, γ (deg.)90.00, 116.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Galactose-binding lectin / Agglutinin / PNA


Mass: 24706.385 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Arachis hypogaea (peanut) / Tissue: seed / References: UniProt: P02872
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.51 %
Crystal growTemperature: 293 K / Method: hanging drop method / pH: 4.6
Details: 30% PEG8000, 0.2M Ammonium sulfate and 0.1M cacodylate, pH 4.6, hanging drop method, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14.2 mg/mlprotein1drop
20.05 Msodium acetate1drop
30.2 M1dropNaCl
40.05 %sodium azide1drop
52.1 mMlactose1drop
612 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 66391 / Num. obs: 64462 / % possible obs: 97.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.16
Reflection shellResolution: 2.7→2.72 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.563 / Num. unique all: 3220 / % possible all: 96.9
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. measured all: 241010 / Rmerge(I) obs: 0.16
Reflection shell
*PLUS
Highest resolution: 2.7 Å / % possible obs: 96.9 % / Num. unique obs: 3220 / Num. measured obs: 12407

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: Isomorphous replacement
Starting model: 1CR7

1cr7


Resolution: 2.7→19.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 172923.68 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.264 3757 6.1 %RANDOM
Rwork0.21 ---
obs0.21 61717 93.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.8604 Å2 / ksol: 0.324339 e/Å3
Displacement parametersBiso mean: 31.5 Å2
Baniso -1Baniso -2Baniso -3
1--4.34 Å20 Å25.15 Å2
2---0.84 Å20 Å2
3---5.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13952 0 16 360 14328
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_mcbond_it6.821.5
X-RAY DIFFRACTIONc_mcangle_it10.682
X-RAY DIFFRACTIONc_scbond_it10.512
X-RAY DIFFRACTIONc_scangle_it14.622.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.357 567 5.9 %
Rwork0.302 8994 -
obs--87.1 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4CARBOHYDRATE.PARAM
X-RAY DIFFRACTION5CIS1.PARAM
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.02

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