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- PDB-4lhn: Structure of the N-terminal domain of the Flo1 adhesin (N-Flo1p) ... -

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Basic information

Entry
Database: PDB / ID: 4lhn
TitleStructure of the N-terminal domain of the Flo1 adhesin (N-Flo1p) from the yeast Saccharomyces cerevisiae, in complex with calcium and mannose
ComponentsFlocculation protein FLO1
KeywordsCELL ADHESION / PA14 domain
Function / homology
Function and homology information


flocculation / fungal-type cell wall / D-mannose binding / side of membrane / cell periphery / extracellular region / plasma membrane
Similarity search - Function
Rubrerythrin, domain 2 - #20 / Rubrerythrin, domain 2 / Flocculin / Flocculin repeat / Jelly Rolls - #1560 / PA14/GLEYA domain / PA14 domain profile. / PA14 domain / PA14 / PA14 domain ...Rubrerythrin, domain 2 - #20 / Rubrerythrin, domain 2 / Flocculin / Flocculin repeat / Jelly Rolls - #1560 / PA14/GLEYA domain / PA14 domain profile. / PA14 domain / PA14 / PA14 domain / Other non-globular / Special / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / Flocculation protein FLO1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.12 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 1.5Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Sep 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 1.7Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flocculation protein FLO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6833
Polymers28,4621
Non-polymers2202
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.700, 63.590, 106.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Flocculation protein FLO1 / Flocculin-1


Mass: 28462.291 Da / Num. of mol.: 1 / Fragment: N-terminal domain,UNP residues 23-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: BY4742 / Gene: FLO1, FLO2, FLO4, FLO8, YAR050W / Plasmid: pET-21b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 (DE3) / References: UniProt: P32768
#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.: 1
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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Protein solution: 50 mM sodium acetate pH 5, 150 mM NaCl, 10 mM CaCl2 Crystallization condition: 1 M NaCl, 15% v/v EtOH, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 16, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.12→15.37 Å / Num. all: 16718 / Num. obs: 16718 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.3
Reflection shellResolution: 2.12→2.23 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 3.7 / Num. unique all: 2106 / % possible all: 80.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
BALBESonline serverphasing
REFMAC5.7.0029refinement
XDSdata reduction
Aimless(CCP4)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XJQ

2xjq


Resolution: 2.12→15.03 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.949 / SU B: 7.088 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19405 839 5 %RANDOM
Rwork0.14602 ---
all0.14838 15840 --
obs0.14838 15840 89.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.134 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.32 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.12→15.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1901 0 13 69 1983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021973
X-RAY DIFFRACTIONr_bond_other_d0.0010.021703
X-RAY DIFFRACTIONr_angle_refined_deg2.0861.9562703
X-RAY DIFFRACTIONr_angle_other_deg0.8983.0043939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5235250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13825.30981
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7615271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.719151
X-RAY DIFFRACTIONr_chiral_restr0.1140.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212279
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02446
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.12→2.174 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 50 -
Rwork0.2 962 -
obs--77.49 %
Refinement TLS params.Method: refined / Origin x: 11.3231 Å / Origin y: 34.0028 Å / Origin z: 21.1677 Å
111213212223313233
T0.014 Å20.0025 Å20.0069 Å2-0.0343 Å20.013 Å2--0.0116 Å2
L0.1731 °2-0.1974 °20.2395 °2-0.4537 °2-0.5353 °2--0.8083 °2
S-0.0283 Å °-0.008 Å °-0.0135 Å °-0.0072 Å °-0.0135 Å °-0.0218 Å °0.0009 Å °0.0107 Å °0.0418 Å °

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