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- PDB-8hyf: Crystal Structure of Banana Lectin In-complex with Fucose at 2.95... -

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Entry
Database: PDB / ID: 8hyf
TitleCrystal Structure of Banana Lectin In-complex with Fucose at 2.95 A Resolution
ComponentsRipening-associated protein
KeywordsSUGAR BINDING PROTEIN / ANTITUMOR PROTEIN
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily
Similarity search - Domain/homology
: / alpha-L-fucopyranose / Ripening-associated protein
Similarity search - Component
Biological speciesMusa x paradisiaca (banana)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsRasheed, S. / Arif, R. / Huda, N. / Ahmad, M.S. / Mateen, S.M.
Funding support1items
OrganizationGrant numberCountry
Not fundedNot funded
CitationJournal: To Be Published
Title: Crystal Structure of Banana Lectin in-Complex with L-Fucose at 2.95 A Resolution
Authors: Rasheed, S. / Arif, R. / Huda, N. / Ahmad, M.S. / Mateen, S.M.
History
DepositionJan 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 2.0Dec 11, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym
Item: _entity.pdbx_number_of_molecules / _pdbx_entry_details.has_protein_modification ..._entity.pdbx_number_of_molecules / _pdbx_entry_details.has_protein_modification / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id
Revision 3.0Oct 22, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Category: atom_site / atom_sites ...atom_site / atom_sites / atom_type / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_contact_author / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_asym / struct_conn / struct_mon_prot_cis / struct_sheet_range
Item: _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] ..._atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_struct_special_symmetry.label_asym_id / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_average_fsc_free / _refine.pdbx_average_fsc_work / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _software.version / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id
Description: Atomic clashes / Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ripening-associated protein
B: Ripening-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,53418
Polymers29,1552
Non-polymers1,37916
Water1,54986
1
B: Ripening-associated protein
hetero molecules

A: Ripening-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,53418
Polymers29,1552
Non-polymers1,37916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_454-x-1,-x+y,-z-1/31
Buried area4030 Å2
ΔGint-73 kcal/mol
Surface area12590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.219, 81.219, 147.315
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-321-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Ripening-associated protein / Banana lectin


Mass: 14577.413 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Musa x paradisiaca (banana) / References: UniProt: O22321
#3: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 100 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#5: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 4.85 Å3/Da / Density % sol: 74.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.25
Details: 1.275 M AMMONIUM SULFATE, 30 mM CADMIUM CHLORIDE, 100 mM TRIS-HCl, PH=8.25
PH range: 8-8.25

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5406 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Nov 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.95→16.96 Å / Num. obs: 12279 / % possible obs: 99.7 % / Redundancy: 1.9 % / Biso Wilson estimate: 30 Å2 / CC1/2: 0.953 / Rmerge(I) obs: 0.144 / Rrim(I) all: 0.203 / Net I/σ(I): 9.2
Reflection shellResolution: 2.95→2.95 Å / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1932 / CC1/2: 0.72 / Rrim(I) all: 0.596

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
PROTEUM3data collection
Aimlessdata scaling
MOLREPphasing
PROTEUM PLUSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BMY

2bmy


Resolution: 2.95→16.956 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.854 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.151 / SU B: 15.092 / SU ML: 0.254 / Average fsc free: 0.9514 / Average fsc work: 0.9688 / Cross valid method: THROUGHOUT / ESU R: 0.511 / ESU R Free: 0.331
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2531 630 5.134 %RANDOM
Rwork0.1923 11640 --
all0.196 ---
obs-12270 99.232 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.039 Å2
Baniso -1Baniso -2Baniso -3
1-0.268 Å20.134 Å20 Å2
2--0.268 Å2-0 Å2
3----0.868 Å2
Refinement stepCycle: LAST / Resolution: 2.95→16.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2046 0 70 86 2202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122156
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161987
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.6572905
X-RAY DIFFRACTIONr_angle_other_deg0.4311.5744582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.6665278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.80256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.84510300
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.1941081
X-RAY DIFFRACTIONr_chiral_restr0.050.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022502
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02494
X-RAY DIFFRACTIONr_nbd_refined0.1980.2378
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2080.21832
X-RAY DIFFRACTIONr_nbtor_refined0.190.21008
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.21171
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.284
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1930.217
X-RAY DIFFRACTIONr_nbd_other0.2230.272
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1820.24
X-RAY DIFFRACTIONr_mcbond_it2.132.7091118
X-RAY DIFFRACTIONr_mcbond_other2.1292.7091118
X-RAY DIFFRACTIONr_mcangle_it3.6324.8581394
X-RAY DIFFRACTIONr_mcangle_other3.6314.8561395
X-RAY DIFFRACTIONr_scbond_it3.1253.2321038
X-RAY DIFFRACTIONr_scbond_other3.0793.2161035
X-RAY DIFFRACTIONr_scangle_it5.2295.7481511
X-RAY DIFFRACTIONr_scangle_other5.1565.7181506
X-RAY DIFFRACTIONr_lrange_it9.13930.32268
X-RAY DIFFRACTIONr_lrange_other9.14630.3442263
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.95-3.0240.354380.2988220.3018620.9060.93199.7680.285
3.024-3.1040.343390.2718130.2748520.9140.9431000.255
3.104-3.1910.374350.2877780.2918130.9070.9411000.263
3.191-3.2860.272400.2487730.2498130.9510.9561000.222
3.286-3.3890.336390.2267490.2317880.9310.9661000.2
3.389-3.5030.268310.2367200.2387520.9580.96499.8670.211
3.503-3.630.304400.2176790.2227220.9380.96999.58450.193
3.63-3.7710.274480.2046670.2097160.9510.97399.86030.175
3.771-3.930.235410.2076440.2096860.9630.97299.85420.175
3.93-4.110.339380.1956150.2036540.9330.97699.84710.166
4.11-4.3190.234330.1715990.1756320.9690.9821000.147
4.319-4.5620.144370.1265620.1275990.9870.991000.107
4.562-4.8520.188340.1145310.1195660.9770.99299.82330.096
4.852-5.2050.186230.1155090.1185320.9760.9911000.097
5.205-5.6490.182300.1324770.1345070.9810.9891000.107
5.649-6.230.164240.1274320.1294560.9890.991000.1
6.23-7.0380.249170.1343980.1384150.9560.9881000.112
7.038-8.270.135120.1453510.1453630.990.9861000.125
8.27-10.5120.226210.1662940.173150.9690.9811000.153
10.512-16.9560.27100.2082270.212370.960.9691000.191

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