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- PDB-5tqz: Frutapin complexed with alpha-D-glucose -

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Basic information

Entry
Database: PDB / ID: 5tqz
TitleFrutapin complexed with alpha-D-glucose
ComponentsFrutapin
KeywordsCarbohydrate-binding protein / Protein / plant lectin
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
alpha-D-glucopyranose / Frutapin
Similarity search - Component
Biological speciesArtocarpus altilis (breadfruit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSousa, F.D. / Guo, J. / Coker, A.R. / Monteiro-Moreira, A.C.O. / Moreira, R.A.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)201016/2015-0 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: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.4Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 1.6Jul 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 1.7Oct 4, 2023Group: 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
Water7,512417
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-29 kcal/mol
Surface area23950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.023, 74.023, 185.522
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 (E. coli) / Strain (production host): 'BL'21-Gold(DE3)pLysS AG / References: UniProt: A0A2D0TC52*PLUS
#2: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


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


Mass: 18.015 Da / Num. of mol.: 417 / 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: 43.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.4 / Details: 0.04 M Potassium monobasic phosphate, 20% 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
ReflectionResolution: 1.6→185.52 Å / Num. obs: 78721 / % possible obs: 100 % / Redundancy: 19.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.205 / Net I/σ(I): 9.3
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 19.5 % / Rmerge(I) obs: 0.2018 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.594 / % possible all: 100

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Processing

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

5krp


Resolution: 1.6→64.11 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.026 / SU ML: 0.055 / Cross valid method: FREE R-VALUE / ESU R: 0.076 / ESU R Free: 0.083 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1918 3914 5 %RANDOM
Rwork0.14907 ---
obs0.15118 74711 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.597 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å2-0 Å2
2---0.02 Å20 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.6→64.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4608 0 48 417 5073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0194978
X-RAY DIFFRACTIONr_bond_other_d0.0020.024609
X-RAY DIFFRACTIONr_angle_refined_deg2.9031.9686789
X-RAY DIFFRACTIONr_angle_other_deg1.339310704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0015650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0723.93201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.21515789
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.011521
X-RAY DIFFRACTIONr_chiral_restr0.1870.2750
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0215666
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021127
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_it1.7731.4072504
X-RAY DIFFRACTIONr_mcbond_other1.7731.4072503
X-RAY DIFFRACTIONr_mcangle_it2.5982.1063159
X-RAY DIFFRACTIONr_mcangle_other2.5982.1063160
X-RAY DIFFRACTIONr_scbond_it2.1551.5992473
X-RAY DIFFRACTIONr_scbond_other2.1551.5992473
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.162.3313622
X-RAY DIFFRACTIONr_long_range_B_refined5.03917.3515285
X-RAY DIFFRACTIONr_long_range_B_other4.9916.9725195
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 309 -
Rwork0.146 5409 -
obs--99.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7444-0.17990.0450.6306-0.07950.4573-0.0050.06030.0699-0.0176-0.0198-0.0857-0.02210.05550.02480.0171-0.00410.00340.05280.01230.0425-5.60711.56913.606
20.80010.0831-0.13950.59570.01460.58720.0058-0.0097-0.0422-0.0004-0.0208-0.05220.0370.07780.0150.01240.00740.0020.04550.00750.0187-6.995-14.95616.983
31.02010.1234-0.08380.7578-0.14720.68250.01170.08750.1209-0.01840.0220.1194-0.0517-0.0863-0.03370.02660.00640.00440.06290.01550.059-41.36113.59916.671
41.22540.04430.14151.01970.07740.55820.0233-0.035-0.05720.0052-0.02940.18770.0188-0.09160.00610.0276-0.0009-0.00170.0651-0.00540.059-42.777-13.11214.528
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 150
2X-RAY DIFFRACTION2B1 - 150
3X-RAY DIFFRACTION3C1 - 150
4X-RAY DIFFRACTION4D1 - 150

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