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- PDB-5o65: Crystal Structure of the Pseudomonas functional amyloid secretion... -

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Basic information

Entry
Database: PDB / ID: 5o65
TitleCrystal Structure of the Pseudomonas functional amyloid secretion protein FapF
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 / SAD / Resolution: 2.5 Å
AuthorsRouse, S.L. / Hare, S. / Lambert, S. / Morgan, R.M.L. / Hawthorne, W.J. / Berry, J. / Matthews, S.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust 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 1.1Nov 13, 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 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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

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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)113,71119
Polymers110,1983
Non-polymers3,51316
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12540 Å2
ΔGint-51 kcal/mol
Surface area38780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.260, 124.731, 80.359
Angle α, β, γ (deg.)90.00, 96.29, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A86 - 404
2010B86 - 404
1020A86 - 404
2020C86 - 404
1030B86 - 404
2030C86 - 404

NCS ensembles :
ID
1
2
3

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Components

#1: Protein FapF


Mass: 36732.570 Da / Num. of mol.: 3
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-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 3.24 Å3/Da / Density % sol: 62.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.05 - 0.1 M sodium citrate, 0.1 M sodium chloride, 20-30 % PEG 400
PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.5→29.38 Å / Num. all: 164859 / Num. obs: 48100 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rpim(I) all: 0.059 / Net I/σ(I): 10.8
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.1 / Rpim(I) all: 0.4 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→2.64 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.908 / SU B: 10.719 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 0.352 / ESU R Free: 0.258 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25928 2467 5.1 %RANDOM
Rwork0.22151 ---
obs0.22343 46008 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.693 Å2
Baniso -1Baniso -2Baniso -3
1-4.8 Å20 Å20.33 Å2
2---0.92 Å20 Å2
3----3.85 Å2
Refinement stepCycle: 1 / Resolution: 2.5→2.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6580 0 199 229 7008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.026918
X-RAY DIFFRACTIONr_bond_other_d0.0070.026497
X-RAY DIFFRACTIONr_angle_refined_deg1.7361.9719317
X-RAY DIFFRACTIONr_angle_other_deg1.522314977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7875839
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52924.462316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.70215984
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8621532
X-RAY DIFFRACTIONr_chiral_restr0.0890.2996
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217733
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021601
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_it2.9354.1683389
X-RAY DIFFRACTIONr_mcbond_other2.9324.1683388
X-RAY DIFFRACTIONr_mcangle_it4.516.244217
X-RAY DIFFRACTIONr_mcangle_other4.5116.2414218
X-RAY DIFFRACTIONr_scbond_it3.8184.7263529
X-RAY DIFFRACTIONr_scbond_other3.8174.7263530
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9696.8825101
X-RAY DIFFRACTIONr_long_range_B_refined8.40434.3477065
X-RAY DIFFRACTIONr_long_range_B_other8.38634.2997013
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A283720.13
12B283720.13
21A286580.14
22C286580.14
31B286400.13
32C286400.13
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 185 -
Rwork0.332 3389 -
obs--99.78 %

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