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- PDB-2xjp: X-ray structure of the N-terminal domain of the flocculin Flo5 fr... -

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Basic information

Entry
Database: PDB / ID: 2xjp
TitleX-ray structure of the N-terminal domain of the flocculin Flo5 from Saccharomyces cerevisiae in complex with calcium and mannose
ComponentsFLOCCULATION PROTEIN FLO5
KeywordsCELL ADHESION / GREENBEARD / PA14-DOMAIN / CARBOHYDRATE BINDING / SOCIAL INTERACTION
Function / homology
Function and homology information


flocculation / fungal-type cell wall / cell-substrate adhesion / D-mannose binding / side of membrane / cell periphery / extracellular region
Similarity search - Function
Rubrerythrin, domain 2 - #20 / Rubrerythrin, domain 2 / Flocculin / Flocculin type 3 repeat / Flocculin repeat / Flocculin type 3 repeat / Jelly Rolls - #1560 / PA14/GLEYA domain / PA14 domain profile. / PA14 domain ...Rubrerythrin, domain 2 - #20 / Rubrerythrin, domain 2 / Flocculin / Flocculin type 3 repeat / Flocculin repeat / Flocculin type 3 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
beta-D-mannopyranose / alpha-D-mannopyranose / Flocculation protein FLO5
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 0.95 Å
AuthorsVeelders, M. / Brueckner, S. / Ott, D. / Unverzagt, C. / Moesch, H.-U. / Essen, L.-O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural Basis of Flocculin-Mediated Social Behavior in Yeast
Authors: Veelders, M. / Brueckner, S. / Ott, D. / Unverzagt, C. / Moesch, H.-U. / Essen, L.-O.
History
DepositionJul 6, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _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_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: FLOCCULATION PROTEIN FLO5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4359
Polymers27,7331
Non-polymers7028
Water8,287460
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.280, 61.820, 106.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein FLOCCULATION PROTEIN FLO5 / FLOCCULIN-5


Mass: 27732.512 Da / Num. of mol.: 1 / Fragment: LECTIN-LIKE FLO5A-DOMAIN, RESIDUES 23-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMI 2 (DE3) / References: UniProt: P38894

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Sugars , 2 types, 3 molecules

#5: 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
#6: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 465 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsD-MANNOSE(MAN): MANNOSE HAS BEEN FOUND IN BOTH ANOMERIC CONFORMATION AS ACCOUNTED BY THE ...D-MANNOSE(MAN): MANNOSE HAS BEEN FOUND IN BOTH ANOMERIC CONFORMATION AS ACCOUNTED BY THE MICROHETEROGENEITY AMAN A1277, BBMA A1278.

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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: 2.75 Å3/Da / Density % sol: 55.27 % / Description: NONE
Crystal growDetails: 0.5 M NACL, 0.1 M BISTRIS PH7.5, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9149
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 24, 2008 / Details: CYLINDRICAL GRAZING INCIDENCE MIRROR
RadiationMonochromator: SI (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9149 Å / Relative weight: 1
ReflectionResolution: 0.95→40.29 Å / Num. obs: 190329 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 7 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 19.6
Reflection shellResolution: 0.95→1 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.8 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDEphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 0.95→20 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.375 / SU ML: 0.009 / Cross valid method: THROUGHOUT / ESU R: 0.014 / ESU R Free: 0.015 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 197 - 199 ARE NOT WELL DEFINED. RESIDUES 200 - 204 HAVE BEEN MODELLED IN TWO DISTINCT CONFORMATIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.12236 3390 1.8 %RANDOM
Rwork0.10523 ---
obs0.10553 186922 99.22 %-
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: 12.246 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2---0.69 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 0.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1926 0 41 460 2427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222466
X-RAY DIFFRACTIONr_bond_other_d0.0010.021830
X-RAY DIFFRACTIONr_angle_refined_deg2.0711.9673452
X-RAY DIFFRACTIONr_angle_other_deg0.98834425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8495362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54725.36197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72915361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.334151
X-RAY DIFFRACTIONr_chiral_restr0.1340.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212922
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02511
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_it3.47121556
X-RAY DIFFRACTIONr_mcbond_other0.4632616
X-RAY DIFFRACTIONr_mcangle_it4.90462571
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.352910
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.8776842
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.1134296
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.95→0.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 218 -
Rwork0.244 12582 -
obs--91.42 %

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