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- PDB-4lhk: Structure of the N-terminal domain of the Lg-Flo1 adhesin (N-Lg-F... -

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Entry
Database: PDB / ID: 4lhk
TitleStructure of the N-terminal domain of the Lg-Flo1 adhesin (N-Lg-Flo1p) from the yeast Saccharomyces pastorianus, in complex with calcium and alpha-1,2-mannobiose
ComponentsFlocculin
KeywordsCELL ADHESION / PA14 domain
Function / homology
Function and homology information


Jelly Rolls - #1560 / PA14/GLEYA domain / PA14 domain profile. / PA14 domain / PA14 / PA14 domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2alpha-alpha-mannobiose / Flocculin
Similarity search - Component
Biological speciesSaccharomyces pastorianus (lager yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsIelasi, F.S. / Willaert, R.G.
Citation
Journal: MBio / Year: 2015
Title: Molecular mechanism of flocculation self-recognition in yeast and its role in mating and survival.
Authors: Goossens, K.V. / Ielasi, F.S. / Nookaew, I. / Stals, I. / Alonso-Sarduy, L. / Daenen, L. / Van Mulders, S.E. / Stassen, C. / van Eijsden, R.G. / Siewers, V. / Delvaux, F.R. / Kasas, S. / ...Authors: Goossens, K.V. / Ielasi, F.S. / Nookaew, I. / Stals, I. / Alonso-Sarduy, L. / Daenen, L. / Van Mulders, S.E. / Stassen, C. / van Eijsden, R.G. / Siewers, V. / Delvaux, F.R. / Kasas, S. / Nielsen, J. / Devreese, B. / Willaert, R.G.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2013
Title: The mannose-specific lectin domains of Flo1p from Saccharomyces cerevisiae and Lg-Flo1p from S. pastorianus: crystallization and preliminary X-ray diffraction analysis of the adhesin-carbohydrate complexes.
Authors: Ielasi, F.S. / Goyal, P. / Sleutel, M. / Wohlkonig, A. / Willaert, R.G.
History
DepositionJul 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Jun 3, 2015Group: Database references
Revision 1.3Dec 2, 2015Group: Database references
Revision 1.4Jun 8, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 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
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flocculin
B: Flocculin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6016
Polymers52,8362
Non-polymers7654
Water4,540252
1
A: Flocculin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8013
Polymers26,4181
Non-polymers3822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Flocculin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8013
Polymers26,4181
Non-polymers3822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.618, 85.476, 68.240
Angle α, β, γ (deg.)90.00, 93.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Flocculin


Mass: 26418.146 Da / Num. of mol.: 2 / Fragment: N-terminal domain,UNP residues 23-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces pastorianus (lager yeast)
Strain: CBS1513 / Gene: Lg-FLO1 / Plasmid: pET-21b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 (DE3) / References: UniProt: B3IUB3
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose / 2alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 2alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsUNIPROT ENTRY B3IUB3 REPORTS A PROLINE AT POSITION 58, WHILE THE AUTHORS HAVE CONFIRMED A GLUTAMINE ...UNIPROT ENTRY B3IUB3 REPORTS A PROLINE AT POSITION 58, WHILE THE AUTHORS HAVE CONFIRMED A GLUTAMINE AT THAT POSITION AND HENCE Q 58 IS A NATURAL VARIANT. THE AUTHORS SAY THAT B3IUB3 ENTRY IN UNIPROT IS NOT COMPLETE AND IT STOPS AT AA 213. FOR AA 214-247, THE SEQUENCE REPORTED HERE IS IDENTICAL TO THE ONE REPORTED FOR UNIPROT B3IUA8.

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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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein solution: 50 mM Tris-HCl pH 7.5, 200 mM NaCl, 10 mM CaCl2 Crystallization condition: 0.1 M amino acids (L-Na-glutamate, DL-alanine, glycine, DL-lysine-HCl, DL-serine), 0.1 M ...Details: Protein solution: 50 mM Tris-HCl pH 7.5, 200 mM NaCl, 10 mM CaCl2 Crystallization condition: 0.1 M amino acids (L-Na-glutamate, DL-alanine, glycine, DL-lysine-HCl, DL-serine), 0.1 M imidazole-MES pH 6.5, 30% w/v PEG 550 MME - PEG 20000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2012
RadiationMonochromator: channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.73→38.54 Å / Num. all: 44852 / Num. obs: 44852 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 9.9
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.704 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2430 / % possible all: 96

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Processing

Software
NameVersionClassification
BALBESonline serverphasing
REFMAC5.7.0029refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XJQ

2xjq


Resolution: 1.73→35.13 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.788 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19329 2275 5.1 %RANDOM
Rwork0.13741 ---
all0.14023 42548 --
obs0.14023 42548 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.116 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å2-0.05 Å2
2--0.07 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.73→35.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 48 252 3672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023524
X-RAY DIFFRACTIONr_bond_other_d0.0010.023076
X-RAY DIFFRACTIONr_angle_refined_deg1.8291.9644828
X-RAY DIFFRACTIONr_angle_other_deg1.133.0027110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8125432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42624.933150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25215500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.724154
X-RAY DIFFRACTIONr_chiral_restr0.1110.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213986
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02798
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.94536600
X-RAY DIFFRACTIONr_sphericity_free31.222594
X-RAY DIFFRACTIONr_sphericity_bonded13.20656681
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 164 -
Rwork0.237 3089 -
obs--95.7 %

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