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- PDB-5m6o: Frutapin complexed with alpha-D-mannose -

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Basic information

Entry
Database: PDB / ID: 5m6o
TitleFrutapin complexed with alpha-D-mannose
ComponentsFrutapin
Keywordscarbohydrate-binding protein / Plant lectin / Complex
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / Frutapin
Similarity search - Component
Biological speciesArtocarpus altilis (breadfruit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
Authorsde Sousa, F.D. / Guo, J. / Coker, A.R. / de Oliveira Monteiro-Moreira, A. / de Azevedo Moreira, R.
Funding support Brazil, 1items
OrganizationGrant numberCountry
National Counsel of Technological and Scientific Development - CNPq201016/2015-0 Brazil
CitationJournal: Biosci. Rep. / Year: 2017
Title: Frutapin, a lectin fromArtocarpus incisa(breadfruit): cloning, expression and molecular insights.
Authors: de Sousa, F.D. / da Silva, B.B. / Furtado, G.P. / Carneiro, I.S. / Lobo, M.D.P. / Guan, Y. / Guo, J. / Coker, A.R. / Lourenzoni, M.R. / Guedes, M.I.F. / Owen, J.S. / Abraham, D.J. / Monteiro- ...Authors: de Sousa, F.D. / da Silva, B.B. / Furtado, G.P. / Carneiro, I.S. / Lobo, M.D.P. / Guan, Y. / Guo, J. / Coker, A.R. / Lourenzoni, M.R. / Guedes, M.I.F. / Owen, J.S. / Abraham, D.J. / Monteiro-Moreira, A.C.O. / Moreira, R.A.
History
DepositionOct 25, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_volume / _citation_author.name
Revision 1.2Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3Jul 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.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Frutapin
B: Frutapin
C: Frutapin
D: Frutapin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8908
Polymers65,1694
Non-polymers7214
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-28 kcal/mol
Surface area24160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.956, 73.956, 185.238
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Frutapin


Mass: 16292.272 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Artocarpus altilis (breadfruit)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A2D0TC52*PLUS
#2: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.17 Å3/Da / Density % sol: 43.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 0.04 M Potassium phosphate monobasic, 16% PEG 8000,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96859 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96859 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.609
11-h,-k,l20.391
ReflectionResolution: 1.7→185.24 Å / Num. obs: 65624 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.133 / Net I/σ(I): 8.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.907 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.614 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5krp

5krp


Resolution: 1.7→64.05 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.375 / SU ML: 0.049 / Cross valid method: FREE R-VALUE / ESU R: 0.018 / ESU R Free: 0.02 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19083 3343 5.1 %RANDOM
Rwork0.14104 ---
obs0.1436 62206 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.775 Å2
Baniso -1Baniso -2Baniso -3
1--4.55 Å2-0 Å2-0 Å2
2---4.55 Å2-0 Å2
3---9.09 Å2
Refinement stepCycle: 1 / Resolution: 1.7→64.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4608 0 48 427 5083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0194927
X-RAY DIFFRACTIONr_bond_other_d0.0020.024570
X-RAY DIFFRACTIONr_angle_refined_deg2.4771.9686715
X-RAY DIFFRACTIONr_angle_other_deg1.175310607
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8995640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29423.909197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.215776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5211520
X-RAY DIFFRACTIONr_chiral_restr0.1470.2746
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0215577
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021111
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_it2.4191.8432479
X-RAY DIFFRACTIONr_mcbond_other2.4181.8422478
X-RAY DIFFRACTIONr_mcangle_it3.5112.7493119
X-RAY DIFFRACTIONr_mcangle_other3.5112.7493120
X-RAY DIFFRACTIONr_scbond_it3.2712.1772448
X-RAY DIFFRACTIONr_scbond_other3.272.1772448
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7933.1373588
X-RAY DIFFRACTIONr_long_range_B_refined6.65322.4445270
X-RAY DIFFRACTIONr_long_range_B_other6.57422.1285171
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 228 -
Rwork0.2 4540 -
obs--99.81 %

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