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- PDB-4mq0: Crystal structure of Parkia biglobosa seed lectin (PBL) in comple... -

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Basic information

Entry
Database: PDB / ID: 4mq0
TitleCrystal structure of Parkia biglobosa seed lectin (PBL) in complex with methyl alpha D-mannopyranoside
ComponentsParkia biglobosa lectin (PBL)
KeywordsSUGAR BINDING PROTEIN / Beta-prism domain / Lectin / carbohydrate binding protein / Protein bodies of seeds
Function / homologyJacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Mainly Beta / methyl alpha-D-mannopyranoside
Function and homology information
Biological speciesParkia biglobosa (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsTeixeira, C.S. / Rocha, B.A.M. / Silva, H.C. / Bari, A.U. / Barroso-Neto, I.L. / Santiago, M.Q. / Nagano, C.S. / Nascimento, K.S. / Debray, H. / Delatorre, P. / Cavada, B.S.
CitationJournal: To be Published
Title: Crystal structure of Parkia biglobosa seed lectin (PBL) in complex with methyl alpha D-mannopyranoside
Authors: Teixeira, C.S. / Rocha, B.A.M. / Silva, H.C. / Bari, A.U. / Barroso-Neto, I.T. / Santiago, M.Q. / Nagano, C.S. / Nascimento, K.S. / Debray, H. / Delatorre, P. / Cavada, B.S.
History
DepositionSep 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Feb 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

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Assembly

Deposited unit
A: Parkia biglobosa lectin (PBL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1954
Polymers47,6131
Non-polymers5833
Water1,63991
1
A: Parkia biglobosa lectin (PBL)
hetero molecules

A: Parkia biglobosa lectin (PBL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3918
Polymers95,2262
Non-polymers1,1656
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3970 Å2
ΔGint4 kcal/mol
Surface area36680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.139, 86.659, 127.857
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Parkia biglobosa lectin (PBL)


Mass: 47612.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Seeds / Source: (natural) Parkia biglobosa (plant)
#2: Sugar ChemComp-MMA / methyl alpha-D-mannopyranoside / O1-METHYL-MANNOSE / methyl alpha-D-mannoside / methyl D-mannoside / methyl mannoside / Methylglucoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
IdentifierTypeProgram
DManp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-mannopyranoseCOMMON NAMEGMML 1.0
o1-methyl-mannoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: NaCl 0.1 M, Bicine 0.1 M, PEG 550 25%, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K

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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: Apr 16, 2013
RadiationMonochromator: Si(111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.12→43.33 Å / Num. obs: 22080 / % possible obs: 94.71 %

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→43.33 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.921 / Cross valid method: THROUGHOUT / ESU R: 0.365 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29272 1197 5.1 %RANDOM
Rwork0.25813 ---
obs0.25992 22080 94.73 %-
all-22080 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.245 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.12→43.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3310 0 39 91 3440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223440
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9051.954664
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3995436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19624.173139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.29715517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.588158
X-RAY DIFFRACTIONr_chiral_restr0.3730.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212615
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6091.52142
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.37523435
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4631298
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6794.51229
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.124→2.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 75 -
Rwork0.346 1326 -
obs--78.53 %

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