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

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Basic information

Entry
Database: PDB / ID: 4ahz
TitleFlo5A showing a heptanuclear gadolinium cluster on its surface after 60 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 / FOURIER SYNTHESIS / Resolution: 1.9 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 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.090, 63.160, 105.420
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 / FLO5A / FLOCCULIN-5


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 90 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.: 252 / 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: 2.64 Å3/Da / Density % sol: 53.41 % / Description: NONE
Crystal growpH: 7.5
Details: 200 MM BISTRIS PROPANE, 500 MM NACL, 3 MM GDAC3, 20% PEG 4000, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 2, 2009 / Details: BENT CYLINDRICAL MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→19.27 Å / Num. obs: 24900 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.2 / % 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: 1.9→19.17 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.919 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 197 - 199 ARE NOT WELL DEFINED. RESIDUES 199 - 204 HAVE BEEN MODELLED IN TWO DISTINCT CONFORMATION
RfactorNum. reflection% reflectionSelection details
Rfree0.20792 450 1.8 %RANDOM
Rwork0.17657 ---
obs0.17714 24449 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.143 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2--1.83 Å20 Å2
3----1.41 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1932 0 13 252 2197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222113
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.952892
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5125284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.62625.51787
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27115295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.317151
X-RAY DIFFRACTIONr_chiral_restr0.0940.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211662
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_it0.6331.51345
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.10522177
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5853768
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4144.5705
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 34 -
Rwork0.226 1769 -
obs--99.72 %

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