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- PDB-6fue: Periplasmic coiled coil domain of the FapF amyloid transporter -

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Basic information

Entry
Database: PDB / ID: 6fue
TitlePeriplasmic coiled coil domain of the FapF amyloid transporter
ComponentsFapF
KeywordsPROTEIN TRANSPORT / Trimeric periplasmic coiled coil
Function / homologyAutotransporter beta-domain superfamily / ISOPROPYL ALCOHOL / FapF
Function and homology information
Biological speciesPseudomonas sp. UK4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.78 Å
AuthorsRouse, S.L. / Stylianou, F. / Morgan, R.M.L. / Matthews, S.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: J. Mol. Biol. / Year: 2018
Title: The FapF Amyloid Secretion Transporter Possesses an Atypical Asymmetric Coiled Coil.
Authors: Rouse, S.L. / Stylianou, F. / Wu, H.Y.G. / Berry, J.L. / Sewell, L. / Morgan, R.M.L. / Sauerwein, A.C. / Matthews, S.
History
DepositionFeb 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _entity.formula_weight
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_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.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FapF
B: FapF
C: FapF
D: FapF
E: FapF
F: FapF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,27824
Polymers27,3616
Non-polymers91818
Water4,918273
1
A: FapF
B: FapF
C: FapF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,11713
Polymers13,6803
Non-polymers43710
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-170 kcal/mol
Surface area7620 Å2
MethodPISA
2
D: FapF
E: FapF
F: FapF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,16111
Polymers13,6803
Non-polymers4818
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-167 kcal/mol
Surface area7210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.590, 37.700, 57.340
Angle α, β, γ (deg.)90.24, 108.95, 119.89
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide
FapF


Mass: 4560.123 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Pseudomonas sp. UK4 (bacteria) / References: UniProt: C4IN73
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Formula: Zn
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.44 Å3/Da / Density % sol: 49.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Zinc acetate dihydrate, 0.1 M Sodium cacodylate, pH 6.5, 10 % v/v 2-Propanol
PH range: 6.2-6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.78→32.01 Å / Num. obs: 22562 / % possible obs: 93.45 % / Redundancy: 1.99 % / Biso Wilson estimate: 29.737 Å2 / CC1/2: 0.9983 / Rmerge(I) obs: 0.0303 / Rpim(I) all: 0.027 / Net I/σ(I): 13.86
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 2 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2263 / CC1/2: 0.833 / Rpim(I) all: 0.282 / Rrim(I) all: 0.42 / % possible all: 93.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
SCALAdata scaling
MoRDaphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.78→32.01 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.269 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.146 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24797 1106 4.9 %RANDOM
Rwork0.20689 ---
obs0.20923 21454 93.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.796 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20.24 Å2-0.38 Å2
2--0.77 Å2-0.4 Å2
3----0.97 Å2
Refinement stepCycle: 1 / Resolution: 1.78→32.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 21 273 2080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191879
X-RAY DIFFRACTIONr_bond_other_d0.0020.021908
X-RAY DIFFRACTIONr_angle_refined_deg1.8562.0022539
X-RAY DIFFRACTIONr_angle_other_deg1.09134365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2645238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.28126.505103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.87715392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4751514
X-RAY DIFFRACTIONr_chiral_restr0.1140.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022131
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02387
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_it3.5733.397913
X-RAY DIFFRACTIONr_mcbond_other3.5593.394912
X-RAY DIFFRACTIONr_mcangle_it4.815.0421137
X-RAY DIFFRACTIONr_mcangle_other4.8115.0461138
X-RAY DIFFRACTIONr_scbond_it4.7993.989966
X-RAY DIFFRACTIONr_scbond_other4.7963.994967
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3365.7961394
X-RAY DIFFRACTIONr_long_range_B_refined10.12632.8127838
X-RAY DIFFRACTIONr_long_range_B_other10.12532.8197839
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.781→1.827 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 109 -
Rwork0.29 1495 -
obs--94.3 %

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