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- PDB-5o68: Crystal Structure of the Pseudomonas functional amyloid secretion... -

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Basic information

Entry
Database: PDB / ID: 5o68
TitleCrystal Structure of the Pseudomonas functional amyloid secretion protein FapF - R157A mutant
ComponentsFapF
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: 3.08 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 1.1May 1, 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

Downloads & links

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Assembly

Deposited unit
A: FapF
B: FapF
C: FapF
D: FapF
E: FapF
F: FapF
G: FapF
H: FapF
I: FapF
J: FapF
K: FapF
L: FapF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)438,83121
Polymers436,38112
Non-polymers2,4509
Water00
1
A: FapF
B: FapF
C: FapF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,31611
Polymers109,0953
Non-polymers2,2208
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-42 kcal/mol
Surface area37990 Å2
MethodPISA
2
D: FapF
E: FapF
F: FapF


Theoretical massNumber of molelcules
Total (without water)109,0953
Polymers109,0953
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-52 kcal/mol
Surface area36980 Å2
MethodPISA
3
G: FapF
H: FapF
I: FapF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,3254
Polymers109,0953
Non-polymers2291
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-54 kcal/mol
Surface area37620 Å2
MethodPISA
4
J: FapF
K: FapF
L: FapF


Theoretical massNumber of molelcules
Total (without water)109,0953
Polymers109,0953
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-48 kcal/mol
Surface area37320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.587, 125.708, 142.667
Angle α, β, γ (deg.)87.09, 84.70, 89.92
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
FapF


Mass: 36365.086 Da / Num. of mol.: 12 / Mutation: R157A
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: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM

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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: 4.02 Å3/Da / Density % sol: 69.42 %
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 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.08→91.7 Å / Num. obs: 94515 / % possible obs: 99.02 % / Redundancy: 3.35 % / Rpim(I) all: 0.103 / Net I/σ(I): 3.49
Reflection shellResolution: 3.08→3.13 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.2 / Rpim(I) all: 0.5 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 5065 / Resolution: 3.08→91.73 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.868 / SU B: 34.4 / SU ML: 0.582 / Cross valid method: THROUGHOUT / ESU R Free: 0.587 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3695 4983 5 %RANDOM
Rwork0.31919 ---
obs0.32175 94515 96.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.567 Å2
Baniso -1Baniso -2Baniso -3
1--7.48 Å20.83 Å20.41 Å2
2---0.52 Å21.01 Å2
3---8 Å2
Refinement stepCycle: 1 / Resolution: 3.08→91.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23665 0 107 0 23772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224308
X-RAY DIFFRACTIONr_bond_other_d0.0020.0221609
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.94133028
X-RAY DIFFRACTIONr_angle_other_deg0.963349506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.89753131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.63124.291988
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.966153301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7181577
X-RAY DIFFRACTIONr_chiral_restr0.0880.23690
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02127983
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025686
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_it2.3214.51912740
X-RAY DIFFRACTIONr_mcbond_other2.3214.51912739
X-RAY DIFFRACTIONr_mcangle_it3.9376.76215799
X-RAY DIFFRACTIONr_mcangle_other3.9376.76215800
X-RAY DIFFRACTIONr_scbond_it2.3394.81411568
X-RAY DIFFRACTIONr_scbond_other2.3394.81511569
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0427.11117230
X-RAY DIFFRACTIONr_long_range_B_refined6.46636.60424848
X-RAY DIFFRACTIONr_long_range_B_other6.46636.60524849
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.079→3.159 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.484 336 -
Rwork0.466 6970 -
obs--95.55 %

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