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- PDB-4ai0: Flo5A showing a heptanuclear gadolinium cluster on its surface af... -

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Basic information

Entry
Database: PDB / ID: 4ai0
TitleFlo5A showing a heptanuclear gadolinium cluster on its surface after 9 min of soaking
ComponentsFLOCCULATION PROTEIN FLO5
KeywordsCELL ADHESION / ADHESIN / FLOCCULIN
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
GADOLINIUM ATOM / Flocculation protein FLO5
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsVeelders, M. / Essen, L.-O.
CitationJournal: Chembiochem / Year: 2012
Title: Complex Gadolinium-Oxo Clusters Formed Along Concave Protein Surfaces.
Authors: Veelders, M. / Essen, L.-O.
History
DepositionFeb 7, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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.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_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.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 FLO5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,89914
Polymers29,0981
Non-polymers1,80113
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.170, 62.690, 105.650
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 FLO5 / FLOCCULIN-5 / FLO5A


Mass: 29097.939 Da / Num. of mol.: 1 / Fragment: LECTIN-LIKE DOMAIN, RESIDUES 23-271
Source method: isolated from a genetically manipulated source
Details: SOAKED 9 MIN WITH GDAC3
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): ORIGAMI 2 / References: UniProt: P38894
#2: Chemical
ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Gd
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

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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: 2.63 Å3/Da / Density % sol: 53.24 % / Description: NONE
Crystal growpH: 7.5
Details: 200 MM BISTRIS PROPANE PH 7.5 500 MM NACL 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.7118
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2010 / Details: BENT CYLINDRICAL MIRROR
RadiationMonochromator: SILICON (1 1 1) CHANNEL- CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7118 Å / Relative weight: 1
ReflectionResolution: 1.8→42.31 Å / Num. obs: 29050 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2XJP

2xjp


Resolution: 1.8→40.58 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.534 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.115 / 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
RfactorNum. reflection% reflectionSelection details
Rfree0.2178 525 1.8 %RANDOM
Rwork0.17646 ---
obs0.17722 28379 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.028 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 13 310 2261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222162
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.9522972
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.175298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7625.49591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21415307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.381152
X-RAY DIFFRACTIONr_chiral_restr0.0980.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211715
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8951.51370
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42622231
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2543792
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.184.5725
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 30 -
Rwork0.26 2002 -
obs--99.61 %

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