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- PDB-1lul: DB58, A LEGUME LECTIN FROM DOLICHOS BIFLORUS -

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Basic information

Entry
Database: PDB / ID: 1lul
TitleDB58, A LEGUME LECTIN FROM DOLICHOS BIFLORUS
ComponentsLECTIN DB58
KeywordsLECTIN / LEGUME LECTIN / QUATERNARY STRUCTURE / PLANT HORMONE BINDING / GLYCOPROTEIN
Function / homology
Function and homology information


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
Biological speciesVigna unguiculata subsp. cylindrica (catjang cowpea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsHamelryck, T.W. / Bouckaert, J. / Dao-Thi, M.H. / Wyns, L. / Etzler, M. / Loris, R.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Carbohydrate binding, quaternary structure and a novel hydrophobic binding site in two legume lectin oligomers from Dolichos biflorus.
Authors: Hamelryck, T.W. / Loris, R. / Bouckaert, J. / Dao-Thi, M.H. / Strecker, G. / Imberty, A. / Fernandez, E. / Wyns, L. / Etzler, M.E.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization of Two Related Lectins from the Legume Plant Dolichos Biflorus
Authors: Dao-Thi, M.-H. / Hamelryck, T.W. / Bouckaert, J. / Korber, F. / Burkow, V. / Poortmans, F. / Etzler, M. / Strecker, G. / Wyns, L. / Loris, R.
History
DepositionJun 30, 1998Processing site: BNL
Revision 1.0Dec 30, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_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_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_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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LECTIN DB58
B: LECTIN DB58
C: LECTIN DB58
D: LECTIN DB58
E: LECTIN DB58
F: LECTIN DB58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,45118
Polymers162,8816
Non-polymers57012
Water00
1
A: LECTIN DB58
B: LECTIN DB58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4846
Polymers54,2942
Non-polymers1904
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-54 kcal/mol
Surface area18220 Å2
MethodPISA
2
C: LECTIN DB58
D: LECTIN DB58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4846
Polymers54,2942
Non-polymers1904
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-54 kcal/mol
Surface area18250 Å2
MethodPISA
3
E: LECTIN DB58
F: LECTIN DB58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4846
Polymers54,2942
Non-polymers1904
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-53 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.390, 130.950, 138.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.30171, -0.2383, 0.92314), (-0.21002, -0.96109, -0.17945), (0.92998, -0.13973, -0.34002)-20.32472, 88.77946, 49.8629
2given(-0.31453, 0.00959, -0.9492), (-0.03114, -0.99951, 0.00022), (-0.94874, 0.02963, 0.31467)52.47976, 80.91944, 37.38261
3given(-0.96648, 0.25668, -0.0051), (0.25036, 0.94672, 0.20258), (0.05683, 0.19451, -0.97925)11.55428, -8.09203, 72.00403
4given(0.89644, 0.19763, 0.39665), (-0.36673, -0.17168, 0.91435), (0.2488, -0.96513, -0.08142)-40.02653, 44.23906, 60.38723
5given(0.57168, -0.79562, -0.20044), (0.07409, 0.29336, -0.95313), (0.81712, 0.53003, 0.22665)14.56052, 46.93898, -14.28682
DetailsDB58 IS A LEGUME LECTIN FROM THE STEMS AND THE LEAVES OF THE TROPICAL LEGUME PLANT DOLICHOS BIFLORUS. IT IS A HETERODIMER THAT CONSISTS OF A TRUNCATED (241 AA) AND AN INTACT SUBUNIT (253 AA). THIS A LOW RESOLUTION STRUCTURE (3.3 ANGSTROM) AND SHOULD BE VIEWED WITH CAUTION. HOWEVER, THE STRUCTURE SHOWS CLEARLY THAT DB58 REPRESENTS THE FOURTH KNOWN LEGUME LECTIN DIMER TYPE, RELATED TO THE PHA-L TYPE TETRAMER. LAST SIX RESIDUES ARE NOT VISIBLE IN THE DENSITY.

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Components

#1: Protein
LECTIN DB58 / DOLICHOS BIFLORUS STEM AND LEAF LECTIN


Mass: 27146.885 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Vigna unguiculata subsp. cylindrica (catjang cowpea)
Organ: STEM AND LEAF / Species: Vigna unguiculata / Strain: subsp. cylindrica / References: UniProt: P19588
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca

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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: 2.6 Å3/Da / Density % sol: 48.1 %
Crystal growpH: 5.6
Details: 100 MM NA-CITRATE PH 5.6 10 % (W/V) PEG 6000 0.3 M NACL
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-7 mg/mlprotein1drop
2100 mMsodium citrate1reservoir
312 %(w/v)PEG60001reservoir
40.2-0.4 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1998 / Details: A/A
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 3.3→20 Å / Num. obs: 22745 / % possible obs: 80.6 % / Observed criterion σ(I): 0 / Redundancy: 2.07 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.135 / Net I/σ(I): 10.2
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 5.5 / % possible all: 68
Reflection
*PLUS
Num. measured all: 47794
Reflection shell
*PLUS
Lowest resolution: 3.33 Å / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BJQ

1bjq


Resolution: 3.3→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: CONSTR / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1797 7.9 %RANDOM
Rwork0.226 ---
obs0.226 22744 80.7 %-
Displacement parametersBiso mean: 53.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10563 0 12 0 10575
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.75
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it5.90.3
X-RAY DIFFRACTIONx_mcangle_it9.190.3
X-RAY DIFFRACTIONx_scbond_it7.360.8
X-RAY DIFFRACTIONx_scangle_it11.650.8
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 3.3→3.42 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.371 153 8.2 %
Rwork0.304 1715 -
obs--68 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.58
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.26
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.75
LS refinement shell
*PLUS
Rfactor obs: 0.304

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