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- PDB-1h9w: Native Dioclea Guianensis seed lectin -

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Basic information

Entry
Database: PDB / ID: 1h9w
TitleNative Dioclea Guianensis seed lectin
ComponentsSEED LECTIN
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 domain / Legume lectin, beta chain, Mn/Ca-binding site / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...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
: / Lectin alpha chain
Similarity search - Component
Biological speciesDIOCLEA GUIANENSIS (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRomero, A. / Wah, D.A. / Sol, F.G.D. / 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 22, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 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 1.4Dec 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SEED LECTIN
B: SEED LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,34712
Polymers50,8422
Non-polymers50510
Water4,864270
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-7.9 kcal/mol
Surface area21680 Å2
MethodPQS
Unit cell
Length a, b, c (Å)90.163, 90.163, 106.755
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.00523, 0.99742, -0.07156), (0.99802, -0.00969, -0.06219), (-0.06272, -0.07109, -0.9955)
Vector: 46.37861, -42.4569, 59.02104)
DetailsBIOLOGICAL_UNIT: HE BIOLOGICALLY ACTIVE UNIT IS ACANONICAL DIMERIC (BELOW PH 6) OR TETRAMER.

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Components

#1: Protein SEED LECTIN


Mass: 25421.053 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) DIOCLEA GUIANENSIS (plant) / Variant: LASIOPHYLLA / Tissue: SEED / References: UniProt: P81637
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS DESCRIBED IN CALVETE ET AL. (1999) BIOCHIM. BIOPHYS. ACTA., 1430, P.367. RESIDUES ...THE SEQUENCE IS DESCRIBED IN CALVETE ET AL. (1999) BIOCHIM. BIOPHYS. ACTA., 1430, P.367. RESIDUES 144 AND 190 (GLY AND SER) ARE NOT SET CORRECTLY IN THE SW DATA BASE.

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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: 2.11 Å3/Da / Density % sol: 41.3 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.6
Details: CRYSTALS WERE GROWN BY THE HANGING DROP VAPOUR DIFFUSION METHOD USING 30% PEG 400, 0.1M ACO, PH 4.6, 10MM CACL2 AND MNCL2
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlprotein1drop
20.1 Msodium acetate1drop
310 mM1dropCaCl2
40.1 Msodium acetate1reservoir
530 %(w/v)PEG4001reservoir
610 mM1dropMnCl2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 2000
RadiationMonochromator: TOROIDAL MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→22 Å / Num. obs: 26619 / % possible obs: 88.7 % / Redundancy: 5.7 % / Biso Wilson estimate: 10.1 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 15.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.089 / Mean I/σ(I) obs: 8 / Rsym value: 0.089 / % possible all: 92.4

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Processing

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

1cvn


Resolution: 2→22.54 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2397478.65 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: SIDE-CHAINS COULD NOT BE ADDED FOR RESIDUES A131, A162, A204, B82, B99 AND B116, AND RESIDUES WERE NOT BUILT FOR B117 AND B237 BECAUSE OF THE LACK OF DENSITY THE RESIDUES 118-122 WERE LEFT ...Details: SIDE-CHAINS COULD NOT BE ADDED FOR RESIDUES A131, A162, A204, B82, B99 AND B116, AND RESIDUES WERE NOT BUILT FOR B117 AND B237 BECAUSE OF THE LACK OF DENSITY THE RESIDUES 118-122 WERE LEFT OUT FOR BOTH MONOMERS BECAUSE OF POOR DENSITY. THE C-TERMINAL RESIDUE ASN237 WAS NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1827 6.9 %RANDOM
Rwork0.228 ---
obs0.228 26599 87.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 78.4159 Å2 / ksol: 0.436914 e/Å3
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å20 Å20 Å2
2---1.18 Å20 Å2
3---2.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 2→22.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3484 0 10 270 3764
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_d25.5
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_it1.521.5
X-RAY DIFFRACTIONc_mcangle_it2.392
X-RAY DIFFRACTIONc_scbond_it2.442
X-RAY DIFFRACTIONc_scangle_it3.552.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.285 322 7 %
Rwork0.232 4258 -
obs--92.1 %
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
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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