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- PDB-2zbj: Crystal structure of Dioclea rostrata lectin -

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Basic information

Entry
Database: PDB / ID: 2zbj
TitleCrystal structure of Dioclea rostrata lectin
ComponentsLectin alpha chain
KeywordsSUGAR BINDING PROTEIN / leguminosae / lectin / diocleinae / dioclea rostrata / Calcium / Manganese / Metal-binding / Vacuole
Function / homology
Function and homology information


positive regulation of histamine secretion by mast cell / aleurone grain / plant-type vacuole / D-mannose binding / 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
: / PHOSPHATE ION / Lectin alpha chain
Similarity search - Component
Biological speciesDioclea rostrata (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
Authorsde Oliveira, T.M. / Delatorre, P. / da Rocha, B.A.M. / de Sousa, E.P. / Nascimento, K.S. / Bezerra, G.A. / Moura, T.R. / Benevides, R.G. / Bezerra, E.H.S. / Moreno, F.B.M.B. ...de Oliveira, T.M. / Delatorre, P. / da Rocha, B.A.M. / de Sousa, E.P. / Nascimento, K.S. / Bezerra, G.A. / Moura, T.R. / Benevides, R.G. / Bezerra, E.H.S. / Moreno, F.B.M.B. / Freire, V.N. / de Azevedo Jr., W.F. / Cavada, B.S.
CitationJournal: J.Struct.Biol. / Year: 2008
Title: Crystal structure of Dioclea rostrata lectin: Insights into understanding the pH-dependent dimer-tetramer equilibrium and the structural basis for carbohydrate recognition in Diocleinae lectins
Authors: de Oliveira, T.M. / Delatorre, P. / da Rocha, B.A.M. / de Souza, E.P. / Nascimento, K.S. / Bezerra, G.A. / Moura, T.R. / Benevides, R.G. / Bezerra, E.H.S. / Moreno, F.B.M.B. / Freire, V.N. / ...Authors: de Oliveira, T.M. / Delatorre, P. / da Rocha, B.A.M. / de Souza, E.P. / Nascimento, K.S. / Bezerra, G.A. / Moura, T.R. / Benevides, R.G. / Bezerra, E.H.S. / Moreno, F.B.M.B. / Freire, V.N. / de Azevedo Jr., W.F. / Cavada, B.S.
History
DepositionOct 22, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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_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)25,7034
Polymers25,5131
Non-polymers1903
Water1,838102
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)102,81316
Polymers102,0534
Non-polymers76012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area8420 Å2
ΔGint-133 kcal/mol
Surface area32470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.511, 88.220, 87.764
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-266-

HOH

21A-291-

HOH

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Components

#1: Protein Lectin alpha chain


Mass: 25513.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: seed lectin / Source: (natural) Dioclea rostrata (plant) / Tissue: seed / References: UniProt: P58908
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Na-HEPES pH 7.5-8.5, 0.4-1.2M sodium potassium tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.05→33.15 Å / Num. all: 15297 / Num. obs: 14526 / % possible obs: 93 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 2.1
Reflection shellResolution: 2.05→2.103 Å / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 2.1 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H9W

1h9w


Resolution: 2.05→33.11 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.83 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2379 766 5 %RANDOM
Rwork0.18679 ---
obs0.18936 14526 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.309 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.05→33.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1764 0 7 102 1873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021815
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9861.952476
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9745230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6424.6675
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.18915277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.227157
X-RAY DIFFRACTIONr_chiral_restr0.130.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021380
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2380.2863
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21257
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2370.2139
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1210.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2670.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4810.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 66 -
Rwork0.239 1063 -
obs--100 %

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