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- PDB-5o67: Crystal structure of the FapF polypeptide transporter - F103A mutant -

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Basic information

Entry
Database: PDB / ID: 5o67
TitleCrystal structure of the FapF polypeptide transporter - F103A mutant
Components(FapF) x 2
KeywordsMEMBRANE PROTEIN / amyloid / secretion / plug / barrel
Function / homologyAutotransporter beta-domain superfamily / FapF
Function and homology information
Biological speciesPseudomonas sp. UK4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsRouse, S.L. / Hare, S. / Lambert, S. / Morgan, R.M.L. / Hawthorne, W.J. / Berry, J. / Matthews, S.J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust100280 United Kingdom
Wellcome Trust104833 United Kingdom
CitationJournal: Nat Commun / Year: 2017
Title: A new class of hybrid secretion system is employed in Pseudomonas amyloid biogenesis.
Authors: Rouse, S.L. / Hawthorne, W.J. / Berry, J.L. / Chorev, D.S. / Ionescu, S.A. / Lambert, S. / Stylianou, F. / Ewert, W. / Mackie, U. / Morgan, R.M.L. / Otzen, D. / Herbst, F.A. / Nielsen, P.H. ...Authors: Rouse, S.L. / Hawthorne, W.J. / Berry, J.L. / Chorev, D.S. / Ionescu, S.A. / Lambert, S. / Stylianou, F. / Ewert, W. / Mackie, U. / Morgan, R.M.L. / Otzen, D. / Herbst, F.A. / Nielsen, P.H. / Dueholm, M. / Bayley, H. / Robinson, C.V. / Hare, S. / Matthews, S.
History
DepositionJun 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FapF
B: FapF
C: FapF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,21011
Polymers109,1433
Non-polymers2,0668
Water23413
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8280 Å2
ΔGint-26 kcal/mol
Surface area40870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.753, 125.816, 81.908
Angle α, β, γ (deg.)90.00, 96.68, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein FapF


Mass: 36393.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. UK4 (bacteria) / Gene: fapF, PSUK4_00060 / Plasmid: PRSF1b / Details (production host): OmpA leader sequence / Production host: Escherichia coli (E. coli) / References: UniProt: C4IN73
#2: Protein FapF


Mass: 36375.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. UK4 (bacteria) / Gene: fapF, PSUK4_00060 / Plasmid: PRSF1b / Details (production host): OmpA leader sequence / Production host: Escherichia coli (E. coli) / References: UniProt: C4IN73
#3: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#4: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.45 Å3/Da / Density % sol: 64.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0/05 - 0.1 M sodium citrate, 0.1 M sodium chloride, 20-30 % PEG400
PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.84→81.35 Å / Num. obs: 33293 / % possible obs: 100 % / Redundancy: 13.4 % / Rpim(I) all: 0.149 / Net I/σ(I): 7.2
Reflection shellResolution: 2.84→2.89 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5o65

5o65


Resolution: 2.84→81.35 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.876 / SU B: 17.699 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R: 0.664 / ESU R Free: 0.381 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29527 1801 5.1 %RANDOM
Rwork0.2316 ---
obs0.23482 33293 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.927 Å2
Baniso -1Baniso -2Baniso -3
1-3.12 Å2-0 Å20.59 Å2
2---0.46 Å2-0 Å2
3----2.73 Å2
Refinement stepCycle: 1 / Resolution: 2.84→81.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6517 0 99 13 6629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.026765
X-RAY DIFFRACTIONr_bond_other_d0.0020.026216
X-RAY DIFFRACTIONr_angle_refined_deg1.7271.9529160
X-RAY DIFFRACTIONr_angle_other_deg0.981314291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3045846
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.43324.467300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.5115994
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2881529
X-RAY DIFFRACTIONr_chiral_restr0.0970.21002
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217705
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021574
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_it2.9714.3943416
X-RAY DIFFRACTIONr_mcbond_other2.9594.3933415
X-RAY DIFFRACTIONr_mcangle_it4.8626.574250
X-RAY DIFFRACTIONr_mcangle_other4.8626.5714251
X-RAY DIFFRACTIONr_scbond_it3.5984.9293349
X-RAY DIFFRACTIONr_scbond_other3.5974.9293350
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0347.1964911
X-RAY DIFFRACTIONr_long_range_B_refined8.7435.3146588
X-RAY DIFFRACTIONr_long_range_B_other8.73735.3176588
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.84→2.914 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 148 -
Rwork0.355 2432 -
obs--99.85 %

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