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- PDB-1h9p: Crystal Structure of Dioclea guianensis Seed Lectin -

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Basic information

Entry
Database: PDB / ID: 1h9p
TitleCrystal Structure of Dioclea guianensis Seed Lectin
ComponentsLECTIN ALPHA CHAIN
KeywordsLECTIN / LEGUME LECTIN OLIGOMERISATION
Function / homology
Function and homology information


D-mannose binding / toxin activity / carbohydrate binding / metal ion binding
Similarity search - Function
Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / : / Lectin alpha chain
Similarity search - Component
Biological speciesDIOCLEA GUIANENSIS (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRomero, A. / Wah, D.A. / Gallego Del sol, F. / Cavada, B.S. / Ramos, M.V. / Grangeiro, T.B. / Sampaio, A.H. / Calvete, J.J.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Crystal Structure of Native and Cd/Cd-Substituted Dioclea Guianensis Seed Lectin. A Novel Manganese-Binding Site and Structural Basis of Dimer-Tetramer Association
Authors: Wah, D.A. / Romero, A. / Gallego, F. / Cavada, B.S. / Ramos, M.V. / Grangeiro, T.B. / Sampaio, A.H. / Calvete, J.J.
#1: Journal: Biochim.Biophys.Acta / Year: 1999
Title: Molecular Characterization and Crystallization of Diocleinae Lectins
Authors: Calvete, J.J. / Thole, H.H. / Raida, M. / Urbanke, C. / Romero, A. / Grangeiro, T.B. / Ramos, M.V. / Almeida, I.M. / Guimaraes, F.N. / Cavada, B.S.
History
DepositionMar 16, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2001Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.status_code_sf / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: LECTIN ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9537
Polymers25,4511
Non-polymers5026
Water2,306128
1
A: LECTIN ALPHA CHAIN
hetero molecules

A: LECTIN ALPHA CHAIN
hetero molecules

A: LECTIN ALPHA CHAIN
hetero molecules

A: LECTIN ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,81328
Polymers101,8044
Non-polymers2,00824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555y,x,-z1
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area9080 Å2
ΔGint-154.6 kcal/mol
Surface area32870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.314, 90.314, 108.276
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-501-

CD

21A-503-

MN

31A-2015-

HOH

41A-2040-

HOH

51A-2107-

HOH

61A-2108-

HOH

71A-2117-

HOH

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Components

#1: Protein LECTIN ALPHA CHAIN / LECTIN BETA CHAIN / LECTIN GAMMA-1 CHAIN / LECTIN GAMMA-2 CHAIN / SEED LECTIN


Mass: 25451.080 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DIOCLEA GUIANENSIS (plant) / Variant: LASIOPHYLLA / Tissue: SEED / References: UniProt: P81637
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Compound detailsD-MANNOSE/D-GLUCOSE-BINDING LECTIN. REQUIRES CA2+ AND MN2+ IONS FOR FULL ACTIVITY.

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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: 2.17 Å3/Da / Density % sol: 42.96 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.4
Details: CRYSTALS WERE GROWN BY THE HANGING DROP VAPOUR DIFFUSION METHOD USING 30% PEG 400, 0.1M MES, PH 6.4 AND 0.1M CDCL2.
Crystal grow
*PLUS
pH: 6.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-12 mg/mlprotein1drop
250 mMMES1drop
310 mM1dropMnCl2
410 mM1dropCaCl2
530 %PEG4001reservoir
60.1 M1reservoirCdCl2
70.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 2000 / Details: BENT MIRROR
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8423 Å / Relative weight: 1
ReflectionResolution: 2→35 Å / Num. obs: 15334 / % possible obs: 99.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 12
Reflection shellResolution: 2→2.11 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 2.5 / % possible all: 96.8
Reflection shell
*PLUS
% possible obs: 96.8 %

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CVN

1cvn


Resolution: 2→34.68 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2755151.35 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 118-121 WERE LEFT OUT BECAUSE OF POOR DENSITY. SIDE CHAINS COULD NOT BE ADDED FOR RESIDUES 117, 122 AND 204 BECAUSE OF THE LACK OF DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1067 7 %RANDOM
Rwork0.239 ---
obs0.239 15323 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.9531 Å2 / ksol: 0.40898 e/Å3
Displacement parametersBiso mean: 36.3 Å2
Baniso -1Baniso -2Baniso -3
1--5.76 Å20 Å20 Å2
2---5.76 Å20 Å2
3---11.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2→34.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1758 0 6 128 1892
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.462
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it2.882.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.367 165 6.9 %
Rwork0.313 2239 -
obs--95.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.299
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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