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- PDB-1bjq: THE DOLICHOS BIFLORUS SEED LECTIN IN COMPLEX WITH ADENINE -

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Basic information

Entry
Database: PDB / ID: 1bjq
TitleTHE DOLICHOS BIFLORUS SEED LECTIN IN COMPLEX WITH ADENINE
ComponentsLECTIN
KeywordsGLYCOPROTEIN / LECTIN / ADENINE / QUATERNARY STRUCTURE / LEGUME LECTIN
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
ADENINE / : / Seed lectin subunit I
Similarity search - Component
Biological speciesVigna unguiculata subsp. cylindrica (catjang cowpea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsHamelryck, T.W. / Loris, R. / Bouckaert, J. / Dao-Thi, M.H. / Wyns, L. / Etzler, M.
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 26, 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 2, 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_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_asym_id / _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_asym_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_asym_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_ref_seq_dif.details / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)218,76232
Polymers216,9218
Non-polymers1,84124
Water00
1
A: LECTIN
B: LECTIN
C: LECTIN
D: LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,38116
Polymers108,4604
Non-polymers92112
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: LECTIN
F: LECTIN
G: LECTIN
H: LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,38116
Polymers108,4604
Non-polymers92112
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.377, 116.135, 224.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(0.36395, -0.54215, -0.75737), (-0.35021, 0.67382, -0.65063), (0.86307, 0.50203, 0.05537)7.38717, 90.99081, -14.59116
2given(0.29801, -0.40533, 0.86423), (-0.57557, 0.64598, 0.50143), (-0.76152, -0.64686, -0.04079)-36.82518, 68.2079, 66.85284
3given(-0.37133, 0.53444, 0.75927), (0.52312, -0.55518, 0.64662), (0.76711, 0.6373, -0.07343)-27.85969, 47.91113, -10.21276
4given(-0.3112, -0.94379, 0.11141), (-0.94752, 0.2991, -0.11287), (0.0732, -0.14069, -0.98734)52.57348, 44.68594, 64.71711
5given(-1, -0.0066, -0.0057), (0.0053, -0.9805, 0.1965), (-0.0069, 0.1964, 0.9805)-20.3164, 140.4834, -14.0178
6given(-0.2983, 0.4087, -0.8626), (0.4004, -0.7668, -0.5017), (-0.8664, -0.495, 0.0651)15.877, 87.3511, 64.9051
7given(0.3142, 0.947, -0.0663), (0.9466, -0.3178, -0.0547), (-0.0729, -0.0455, -0.9963)-75.1321, 108.3493, 56.4041

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Components

#1: Protein
LECTIN / DBL


Mass: 27115.078 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: DOLICHOS BIFLORUS SEED LECTIN
Source: (gene. exp.) Vigna unguiculata subsp. cylindrica (catjang cowpea)
Species: Vigna unguiculata / Strain: subsp. cylindrica / Cell line: BL21 / Organ: SEEDS / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P05045
#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: Chemical
ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H5N5
Compound detailsTHE DOLICHOS BIFLORUS SEED LECTIN IS A HETEROTETRAMERIC LEGUME LECTIN COMPOSED OF TWO INTACT (253 ...THE DOLICHOS BIFLORUS SEED LECTIN IS A HETEROTETRAMERIC LEGUME LECTIN COMPOSED OF TWO INTACT (253 AA) AND TWO TRUNCATED SUBUNITS (244 AA). ONLY 235 RESIDUES ARE VISIBLE IN THE ELECTRON DENSITY FOR THE TRUNCATED SUBUNITS (C, D, E AND F). THE ASYMMETRIC UNIT CONTAINS TWO TETRAMERS (CHAINS ABCD AND EFGH).

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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: 2.41 Å3/Da / Density % sol: 40 %
Crystal growpH: 6.5
Details: 100 MM NA-CACODYLATE PH 6.5 10 % (W/V) PEG 8000 20 MM MGAC2 1 MM ADENINE
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Dao-Thi, M., (1998) Acta Crystallogr.,Sect.D, 54, 1446.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
2100 mMsodium cacodylate1reservoir
38-12 %(w/v)PEG80001reservoir
420 mM1reservoirMgAc2
51
61
71

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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
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.65→20 Å / Num. obs: 57851 / % possible obs: 92.4 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 12.3
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 6.5 / % possible all: 69.1
Reflection
*PLUS
Num. measured all: 162686
Reflection shell
*PLUS
Lowest resolution: 2.67 Å / Mean I/σ(I) obs: 2.5

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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 1FAT

1fat


Resolution: 2.65→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.246 5889 10.2 %RANDOM
Rwork0.219 ---
obs0.219 57851 92.5 %-
Displacement parametersBiso mean: 26 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14602 0 96 0 14698
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.67
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.450.35
X-RAY DIFFRACTIONx_mcangle_it2.490.35
X-RAY DIFFRACTIONx_scbond_it1.450.4
X-RAY DIFFRACTIONx_scangle_it2.130.4
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev Biso (Å2)Rms dev position (Å)
11RESTRAINTSX-RAY DIFFRACTION00
22X-RAY DIFFRACTION00
33X-RAY DIFFRACTION00
44X-RAY DIFFRACTION00
LS refinement shellResolution: 2.65→2.74 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.359 432 10 %
Rwork0.326 3888 -
obs--70.2 %
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
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.46
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.45
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.67
LS refinement shell
*PLUS
Rfactor obs: 0.326

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