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- PDB-4uys: X-ray structure of the N-terminal domain of the flocculin Flo11 f... -

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Basic information

Entry
Database: PDB / ID: 4uys
TitleX-ray structure of the N-terminal domain of the flocculin Flo11 from Saccharomyces cerevisiae
ComponentsFLOCCULATION PROTEIN FLO11
KeywordsCELL ADHESION / ADHESIN / FLOCCULATION / HYDROPHOBIC PATCHES / HOMOTYPIC BINDING
Function / homology
Function and homology information


cell-cell self recognition / single-species surface biofilm formation / flocculation / pseudohyphal growth / invasive growth in response to glucose limitation / homotypic cell-cell adhesion / filamentous growth / cellular bud neck / fungal-type vacuole / cell adhesion involved in single-species biofilm formation ...cell-cell self recognition / single-species surface biofilm formation / flocculation / pseudohyphal growth / invasive growth in response to glucose limitation / homotypic cell-cell adhesion / filamentous growth / cellular bud neck / fungal-type vacuole / cell adhesion involved in single-species biofilm formation / side of membrane / cell-cell adhesion / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Flocculin 11 domain / Flo11 domain / Flocculin 11 (Flo11) domain profile. / Flo11
Similarity search - Domain/homology
Flocculation protein FLO11
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsKraushaar, T. / Veelders, M. / Brueckner, S. / Rhinow, D. / Moesch, H.U. / Essen, L.O.
CitationJournal: Structure / Year: 2015
Title: Interactions by the Fungal Flo11 Adhesin Depend on a Fibronectin Type III-Like Adhesin Domain Girdled by Aromatic Bands.
Authors: Kraushaar, T. / Bruckner, S. / Veelders, M. / Rhinow, D. / Schreiner, F. / Birke, R. / Pagenstecher, A. / Mosch, H. / Essen, L.
History
DepositionSep 3, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FLOCCULATION PROTEIN FLO11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7499
Polymers20,5631
Non-polymers1858
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.720, 101.550, 33.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2055-

HOH

21A-2126-

HOH

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Components

#1: Protein FLOCCULATION PROTEIN FLO11 / FLOCCULIN-11 / MUCIN-LIKE PROTEIN 1 / FLO11


Mass: 20563.312 Da / Num. of mol.: 1 / Fragment: FLO11 DOMAIN, UNP RESIDUES 30-211
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SHUFFLE T7 EXPRESS / References: UniProt: P08640
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.25 Å3/Da / Density % sol: 45.45 % / Description: NONE
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 100 MM NAHEPES, PH 7.5, 100 MM MGCL2, 30% PEG 400, THEN SOAKED IN THIS CONDITION CONTAINING 50 MM CACL2 ADDITIONALLY FOR 5 MIN; FOR CRYOPROTECTION THE PROTEIN ...Details: PROTEIN WAS CRYSTALLIZED FROM 100 MM NAHEPES, PH 7.5, 100 MM MGCL2, 30% PEG 400, THEN SOAKED IN THIS CONDITION CONTAINING 50 MM CACL2 ADDITIONALLY FOR 5 MIN; FOR CRYOPROTECTION THE PROTEIN WAS SOAKED IN THE LATTER CONDITION CONTAINING 35% PEG 400 INSTEAD OF 30%.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.799905
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2013 / Details: MIRRORS
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.799905 Å / Relative weight: 1
ReflectionResolution: 1.05→28.5 Å / Num. obs: 85769 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.4
Reflection shellResolution: 1.05→1.11 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
PHENIXAUTOMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.05→28.51 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.959 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.16968 1081 1.3 %RANDOM
Rwork0.14683 ---
obs0.1471 84603 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20 Å20 Å2
2---1.45 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.05→28.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1416 0 8 280 1704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021518
X-RAY DIFFRACTIONr_bond_other_d0.0010.021290
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.8952090
X-RAY DIFFRACTIONr_angle_other_deg0.9253.0042974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3826.37580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.55515226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1090.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021848
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02390
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_it0.9561.017743
X-RAY DIFFRACTIONr_mcbond_other0.9541.011742
X-RAY DIFFRACTIONr_mcangle_it1.2321.529939
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.61.19775
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_restr2.532808
X-RAY DIFFRACTIONr_sphericity_free84.443568
X-RAY DIFFRACTIONr_sphericity_bonded12.10152982
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 71 -
Rwork0.308 6166 -
obs--99.79 %

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