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

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Basic information

Entry
Database: PDB / ID: 4uyt
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
ACETATE ION / Flocculation protein FLO11
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.03 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 1.1Oct 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_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)20,7608
Polymers20,5631
Non-polymers1977
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.430, 54.850, 120.150
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 / FLO11 / FLOCCULIN-11 / MUCIN-LIKE PROTEIN 1


Mass: 20563.312 Da / Num. of mol.: 1 / Fragment: FLO11 DOMAIN, 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) / 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.: 6 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.49 Å3/Da / Density % sol: 50.68 % / Description: NONE
Crystal growpH: 6
Details: PROTEIN WAS CRYSTALLIZED FROM 100 MM NA3CITRATE2H2O, PH 6.0, 1 M LI2SO4, 4% PEG 4000; THEN SOAKED IN THIS CONDITION CONTAINING 25 % GLYCERIN ADDITIONALLY FOR CRYOPROTECTION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409
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: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.03→40.46 Å / Num. obs: 98507 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 18.7
Reflection shellResolution: 1.03→1.09 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.6 / % possible all: 93.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
PHENIXAUTOMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.03→40.54 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.636 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.14416 1239 1.3 %RANDOM
Rwork0.12863 ---
obs0.12882 97267 98.31 %-
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: 14.774 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.65 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.03→40.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1416 0 10 284 1710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021540
X-RAY DIFFRACTIONr_bond_other_d0.0010.021303
X-RAY DIFFRACTIONr_angle_refined_deg1.431.8942118
X-RAY DIFFRACTIONr_angle_other_deg0.753.0043000
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6315194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24426.54884
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.1415229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021895
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02399
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_it1.0781.151753
X-RAY DIFFRACTIONr_mcbond_other1.071.146751
X-RAY DIFFRACTIONr_mcangle_it1.3971.73954
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8311.381787
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_restr2.48932843
X-RAY DIFFRACTIONr_sphericity_free56.703586
X-RAY DIFFRACTIONr_sphericity_bonded14.23853012
LS refinement shellResolution: 1.031→1.058 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 73 -
Rwork0.297 6434 -
obs--88.72 %

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