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- PDB-6fhd: Crystal Structure of the Amyloid-like, out-of-register beta-sheet... -

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Basic information

Entry
Database: PDB / ID: 6fhd
TitleCrystal Structure of the Amyloid-like, out-of-register beta-sheets, polymorph of the LFKFFK segment from the S. aureus PSMalpha3
ComponentsPsm alpha-3
KeywordsPROTEIN FIBRIL / Out-of-register beta-sheets / amyloid-like / bacterial amyloid fibril / S. aureus / PSM
Function / homologyPhenol-soluble modulin alpha peptide / Phenol-soluble modulin alpha peptide family / killing of cells of another organism / Phenol-soluble modulin PSM-alpha-3
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
Model detailsPhenol Soluble Modulin
AuthorsLandau, M. / Salinas, N.
Funding support Israel, 4items
OrganizationGrant numberCountry
Israel Science Foundation560/16 Israel
Deutsch-IsraelischeProjektkooperation (DIP)3655/1-1 Israel
I-CORE Program of the Planning and Budgeting Committee and The Israel Science Foundation1775/12 Israel
United States - Israel Binational Science Foundation (BSF)2013254 Israel
CitationJournal: Nat Commun / Year: 2018
Title: Extreme amyloid polymorphism in Staphylococcus aureus virulent PSM alpha peptides.
Authors: Salinas, N. / Colletier, J.P. / Moshe, A. / Landau, M.
History
DepositionJan 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Psm alpha-3
A: Psm alpha-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,8775
Polymers1,6622
Non-polymers2153
Water905
1
B: Psm alpha-3
A: Psm alpha-3
hetero molecules

B: Psm alpha-3
A: Psm alpha-3
hetero molecules

B: Psm alpha-3
A: Psm alpha-3
hetero molecules

B: Psm alpha-3
A: Psm alpha-3
hetero molecules

B: Psm alpha-3
A: Psm alpha-3
hetero molecules

B: Psm alpha-3
A: Psm alpha-3
hetero molecules

B: Psm alpha-3
A: Psm alpha-3
hetero molecules

B: Psm alpha-3
A: Psm alpha-3
hetero molecules

B: Psm alpha-3
A: Psm alpha-3
hetero molecules

B: Psm alpha-3
A: Psm alpha-3
hetero molecules

B: Psm alpha-3
A: Psm alpha-3
hetero molecules

B: Psm alpha-3
A: Psm alpha-3
hetero molecules

B: Psm alpha-3
A: Psm alpha-3
hetero molecules

B: Psm alpha-3
A: Psm alpha-3
hetero molecules

B: Psm alpha-3
A: Psm alpha-3
hetero molecules

B: Psm alpha-3
A: Psm alpha-3
hetero molecules

B: Psm alpha-3
A: Psm alpha-3
hetero molecules

B: Psm alpha-3
A: Psm alpha-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,79090
Polymers29,91836
Non-polymers3,87254
Water64936
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_535x,y-2,z1
crystal symmetry operation1_525x,y-3,z1
crystal symmetry operation1_515x,y-4,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation1_585x,y+3,z1
crystal symmetry operation1_595x,y+4,z1
crystal symmetry operation4_748-x+5/2,y-1/2,-z+31
crystal symmetry operation4_758-x+5/2,y+1/2,-z+31
crystal symmetry operation4_738-x+5/2,y-3/2,-z+31
crystal symmetry operation4_728-x+5/2,y-5/2,-z+31
crystal symmetry operation4_718-x+5/2,y-7/2,-z+31
crystal symmetry operation4_768-x+5/2,y+3/2,-z+31
crystal symmetry operation4_778-x+5/2,y+5/2,-z+31
crystal symmetry operation4_788-x+5/2,y+7/2,-z+31
crystal symmetry operation4_798-x+5/2,y+9/2,-z+31
Unit cell
Length a, b, c (Å)41.030, 11.730, 24.610
Angle α, β, γ (deg.)90.000, 121.890, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-102-

NA

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Components

#1: Protein/peptide Psm alpha-3


Mass: 831.054 Da / Num. of mol.: 2
Fragment: LFKFFK from PSMalpha3 (residues 7-12) secreted by S. aureus
Source method: obtained synthetically / Details: LFKFFK from PSMalpha3, synthesized / Source: (synth.) Staphylococcus aureus (bacteria) / References: UniProt: H9BRQ7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 1.52 Å3/Da / Density % sol: 18.96 % / Description: Needle-like
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Reservoir contained 0.1 M Sodium acetate pH 5.1 , 45 %w/v PEG 400, 0.09 M LiSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.85→19.3 Å / Num. obs: 913 / % possible obs: 96.3 % / Redundancy: 17.636 % / Biso Wilson estimate: 19.453 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.284 / Rrim(I) all: 0.292 / Χ2: 0.851 / Net I/σ(I): 9.07
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.9617.50.5475.611480.9460.56391.9
1.96-2.118.4210.3727.631330.9490.383100
2.1-2.2717.6280.338.61290.9860.3499.2
2.27-2.4816.7460.3298.031140.9790.3494.2
2.48-2.7818.1760.3019.471080.9890.31199.1
2.78-3.218.4180.26111.19910.9750.26897.8
3.2-3.9217.8440.22812.77900.9940.23495.7
3.92-5.5517.1380.27313.48650.9930.28197
5.55-19.314.8570.2199.71350.9980.23287.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ideal beta-strand of poly-alanine

Resolution: 1.85→19.3 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.435 / SU ML: 0.097 / SU R Cruickshank DPI: 0.2321 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.232 / ESU R Free: 0.147
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1869 92 10.1 %RANDOM
Rwork0.1712 ---
obs0.1728 821 97.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 34.14 Å2 / Biso mean: 11.819 Å2 / Biso min: 6.87 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å2-0 Å20.02 Å2
2---0.53 Å2-0 Å2
3----0.38 Å2
Refinement stepCycle: final / Resolution: 1.85→19.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms120 0 11 5 136
Biso mean--28.99 23.51 -
Num. residues----12
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02132
X-RAY DIFFRACTIONr_bond_other_d0.0350.02132
X-RAY DIFFRACTIONr_angle_refined_deg1.8932.05172
X-RAY DIFFRACTIONr_angle_other_deg2.5083302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.292510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.695206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.1161526
X-RAY DIFFRACTIONr_chiral_restr0.0970.216
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02120
X-RAY DIFFRACTIONr_gen_planes_other0.0190.0240
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 8 -
Rwork0.297 73 -
all-81 -
obs--98.78 %

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