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- PDB-5j76: Structure of Lectin from Colocasia esculenta(L.) Schott -

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Basic information

Entry
Database: PDB / ID: 5j76
TitleStructure of Lectin from Colocasia esculenta(L.) Schott
Components(12kD storage protein) x 2
KeywordsSUGAR BINDING PROTEIN / Sugar Binding / Lectin / Colocasia agglutinin
Function / homology
Function and homology information


response to other organism / D-mannose binding / extracellular region
Similarity search - Function
Agglutinin, subunit A / Bulb-type lectin domain / Bulb-type lectin domain / Bulb-type lectin domain superfamily / Bulb-type lectin domain profile. / Bulb-type mannose-specific lectin / Orthogonal Prism / Mainly Beta
Similarity search - Domain/homology
Mannose-specific lectin 1
Similarity search - Component
Biological speciesColocasia esculenta (taro)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsVajravijayan, S. / Pletnev, S. / Nandhagopal, N. / Gunasekaran, K.
CitationJournal: Int.J.Biol.Macromol. / Year: 2016
Title: Structural analysis of beta-prism lectin from Colocasia esculenta (L.) S chott.
Authors: Vajravijayan, S. / Pletnev, S. / Pletnev, V.Z. / Nandhagopal, N. / Gunasekaran, K.
History
DepositionApr 6, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 12kD storage protein
B: 12kD storage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5784
Polymers24,3942
Non-polymers1842
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-32 kcal/mol
Surface area10290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.471, 75.471, 121.177
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-354-

HOH

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Components

#1: Protein 12kD storage protein


Mass: 11958.227 Da / Num. of mol.: 1 / Fragment: UNP residues 28-136 / Source method: isolated from a natural source / Source: (natural) Colocasia esculenta (taro) / References: UniProt: Q39487
#2: Protein 12kD storage protein


Mass: 12435.870 Da / Num. of mol.: 1 / Fragment: UNP residues 144-254 / Source method: isolated from a natural source / Source: (natural) Colocasia esculenta (taro) / References: UniProt: Q39487
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.08 Å3/Da / Density % sol: 69.88 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 4 / Details: 2.7M Na Malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→65.3 Å / Num. obs: 23782 / % possible obs: 99.8 % / Redundancy: 5.3 % / Rsym value: 0.095 / Net I/σ(I): 20.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.3 % / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MEZ

3mez


Resolution: 2.1→28.76 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.916 / SU ML: 0.099 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.124
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2044 1200 5 %RANDOM
Rwork0.1645 ---
obs0.1665 22646 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 129.76 Å2 / Biso mean: 56.505 Å2 / Biso min: 38.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 2.1→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 12 92 1822
Biso mean--74.25 62.22 -
Num. residues----220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191770
X-RAY DIFFRACTIONr_bond_other_d0.0030.021624
X-RAY DIFFRACTIONr_angle_refined_deg2.051.9362397
X-RAY DIFFRACTIONr_angle_other_deg1.09133734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0735218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.47725.28787
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45215282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.788156
X-RAY DIFFRACTIONr_chiral_restr0.1430.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022041
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02425
X-RAY DIFFRACTIONr_mcbond_it4.6515.321878
X-RAY DIFFRACTIONr_mcbond_other4.6165.316877
X-RAY DIFFRACTIONr_mcangle_it5.8367.941094
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 85 -
Rwork0.269 1618 -
all-1703 -
obs--98.5 %

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