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

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Basic information

Entry
Database: PDB / ID: 4uyr
TitleX-ray structure of the N-terminal domain of the flocculin Flo11 from Saccharomyces cerevisiae
ComponentsFLOCCULATION PROTEIN FLO11
KeywordsCELL ADHESION / SACCHAROMYCES CEREVISIAE / FLO11 / 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
PHOSPHATE ION / Flocculation protein FLO11
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 0.89 Å
AuthorsVeelders, M. / Kraushaar, T. / 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 1.1Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Oct 23, 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_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.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_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_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)23,9145
Polymers23,7491
Non-polymers1654
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.450, 54.830, 121.910
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 FLO11 / FLOCCULIN-11 / MUCIN-LIKE PROTEIN 1 / FLO11


Mass: 23748.949 Da / Num. of mol.: 1 / Fragment: FLO11 DOMAIN, UNP RESIDUES 22-211
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / 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.: 2 / 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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.2 Å3/Da / Density % sol: 44.06 % / Description: NONE
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 30% PEG 400, 100 MM MGCL2, 100 MM NAHEPES, PH 7.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.70847
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2011 / Details: MIRRORS
RadiationMonochromator: SI(311) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.70847 Å / Relative weight: 1
ReflectionResolution: 0.89→40.76 Å / Num. obs: 156350 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.1
Reflection shellResolution: 0.89→0.94 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
SHELXCDEphasing
ARP/wARPphasing
REFMAC5.7.0032refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 0.89→40.76 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.374 / SU ML: 0.01 / Cross valid method: THROUGHOUT / ESU R: 0.013 / ESU R Free: 0.013 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.13399 4675 3 %RANDOM
Rwork0.12677 ---
obs0.12699 151392 99.34 %-
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: 15.747 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2---0.13 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 0.89→40.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1503 0 8 239 1750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191647
X-RAY DIFFRACTIONr_bond_other_d0.0010.021385
X-RAY DIFFRACTIONr_angle_refined_deg1.761.8862275
X-RAY DIFFRACTIONr_angle_other_deg0.8923.0043205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6125218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.98726.11190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.9815244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1040.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022008
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02434
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_it1.7391.22794
X-RAY DIFFRACTIONr_mcbond_other1.6451.215793
X-RAY DIFFRACTIONr_mcangle_it2.0991.8351002
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0111.467853
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_restr3.69833032
X-RAY DIFFRACTIONr_sphericity_free64.203573
X-RAY DIFFRACTIONr_sphericity_bonded21.24853163
LS refinement shellResolution: 0.89→0.913 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 359 -
Rwork0.301 10997 -
obs--99.22 %

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