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- PDB-4not: Crystal structure of Dioclea sclerocarpa lectin complexed with X-man -

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Basic information

Entry
Database: PDB / ID: 4not
TitleCrystal structure of Dioclea sclerocarpa lectin complexed with X-man
ComponentsLectin alpha chain
KeywordsSUGAR BINDING PROTEIN / Jelly-roll motif / Lectin / Carbohydrate/Sugar Binding
Function / homology
Function and homology information


aleurone grain / glucose binding / vacuole / mannose binding / manganese ion binding / calcium 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
: / Chem-XMM / Lectin alpha chain
Similarity search - Component
Biological speciesDioclea sclerocarpa (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsBarroso-Neto, I.L. / Teixeira, C.S. / Correia, J.L.A. / Santiago, M.Q. / Pinto-Junior, V.R. / Osterne, V.J.S. / Plinio, D. / Rocha, B.A.M. / Cavada, B.S.
CitationJournal: To be Published
Title: Crystal structure of Dioclea sclerocarpa lectin complexed with X-man
Authors: Barroso-Neto, I.L. / Teixeira, C.S. / Correia, J.L.A. / Santiago, M.Q. / Pinto-Junior, V.R. / Osterne, V.J.S. / Plinio, D. / Rocha, B.A.M. / Cavada, B.S.
History
DepositionNov 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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_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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)26,1354
Polymers25,6311
Non-polymers5043
Water1,62190
1
A: Lectin alpha chain
hetero molecules

A: Lectin alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2708
Polymers51,2632
Non-polymers1,0076
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area1660 Å2
ΔGint-5 kcal/mol
Surface area18760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.940, 66.610, 108.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Lectin alpha chain / DSL / Lectin beta chain / Lectin gamma chain


Mass: 25631.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: seed / Source: (natural) Dioclea sclerocarpa (plant) / References: UniProt: B3EWJ2
#2: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Sugar ChemComp-XMM / 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside / (2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL / (5-BROMO-4-CHLORO-3-INDOLYL)-Alpha-D-MANNOSE / 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannoside / 5-bromo-4-chloro-1H-indol-3-yl D-mannoside / 5-bromo-4-chloro-1H-indol-3-yl mannoside


Type: D-saccharide / Mass: 408.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H15BrClNO6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.5 M Ammonium sulfate; 0.1 M Sodium citrate tribasic dihydrate; 1.3 M Lithium sulfate monohydrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 1, 2013
RadiationMonochromator: Double Flat Crystal Monochromator with Fixed-exit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.35→56.788 Å / Num. all: 134440 / Num. obs: 10134 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 27.962 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 10.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.35-2.484.60.2053.4680014730.205100
2.48-2.634.60.1764635213690.176100
2.63-2.814.60.1464.6598813030.146100
2.81-3.034.50.1155.1541612110.115100
3.03-3.324.40.0946.2495911240.094100
3.32-3.724.30.0727.6434410190.072100
3.72-4.294.10.0637.737049020.06399.9
4.29-5.254.20.0666.632917790.06699.9
5.25-7.434.50.0738.127526150.07399.9
7.43-28.3944.10.05211.914063390.05294

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.35 Å28.39 Å
Translation2.35 Å28.39 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASER2.5.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
MAR345data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→28.41 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.874 / WRfactor Rfree: 0.2632 / WRfactor Rwork: 0.2242 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8163 / SU R Cruickshank DPI: 0.4858 / SU Rfree: 0.2727 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.486 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2565 490 4.8 %RANDOM
Rwork0.2094 ---
all0.2115 ---
obs0.2115 10134 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.42 Å2 / Biso mean: 28.4613 Å2 / Biso min: 14.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.55 Å2-0 Å2-0 Å2
2---2.54 Å20 Å2
3----3.01 Å2
Refinement stepCycle: LAST / Resolution: 2.35→28.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1790 0 25 90 1905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191856
X-RAY DIFFRACTIONr_bond_other_d00.021697
X-RAY DIFFRACTIONr_angle_refined_deg1.9271.9572531
X-RAY DIFFRACTIONr_angle_other_deg3.80633918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3965232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.86824.54577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.79615286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.949157
X-RAY DIFFRACTIONr_chiral_restr0.1190.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212102
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02423
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 36 -
Rwork0.238 710 -
all-746 -
obs--100 %

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