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- PDB-6fhc: Crystal Structure of the Amyloid-like hexametric polymorph of the... -

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Basic information

Entry
Database: PDB / ID: 6fhc
TitleCrystal Structure of the Amyloid-like hexametric polymorph of the LFKFFK segment from the S. aureus PSMalpha3
ComponentsPsm alpha-3
KeywordsPROTEIN FIBRIL / Hexamer / 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 / CARBONATE ION / THIOCYANATE ION / Phenol-soluble modulin PSM-alpha-3
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.51 Å
Model detailsPhenol Soluble Modulin
AuthorsLandau, M. / Colletier, J.-P.
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

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Assembly

Deposited unit
A: Psm alpha-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,1795
Polymers8311
Non-polymers3484
Water905
1
A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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A: Psm alpha-3
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Theoretical massNumber of molelcules
Total (without water)63,656270
Polymers44,87754
Non-polymers18,780216
Water97354
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation1_557x,y,z+21
crystal symmetry operation1_558x,y,z+31
crystal symmetry operation1_559x,y,z+41
crystal symmetry operation6_558x-y,x,z+23/61
crystal symmetry operation1_551x,y,z-41
crystal symmetry operation1_552x,y,z-31
crystal symmetry operation6_551x-y,x,z-19/61
crystal symmetry operation1_553x,y,z-21
crystal symmetry operation6_552x-y,x,z-13/61
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation6_553x-y,x,z-7/61
crystal symmetry operation2_555-y,x-y,z+2/31
crystal symmetry operation2_556-y,x-y,z+5/31
crystal symmetry operation2_557-y,x-y,z+8/31
crystal symmetry operation2_558-y,x-y,z+11/31
crystal symmetry operation2_559-y,x-y,z+14/31
crystal symmetry operation2_551-y,x-y,z-10/31
crystal symmetry operation2_552-y,x-y,z-7/31
crystal symmetry operation2_553-y,x-y,z-4/31
crystal symmetry operation2_554-y,x-y,z-1/31
crystal symmetry operation3_555-x+y,-x,z+1/31
crystal symmetry operation3_556-x+y,-x,z+4/31
crystal symmetry operation3_557-x+y,-x,z+7/31
crystal symmetry operation3_558-x+y,-x,z+10/31
crystal symmetry operation3_559-x+y,-x,z+13/31
crystal symmetry operation3_551-x+y,-x,z-11/31
crystal symmetry operation3_552-x+y,-x,z-8/31
crystal symmetry operation3_553-x+y,-x,z-5/31
crystal symmetry operation3_554-x+y,-x,z-2/31
crystal symmetry operation4_555-x,-y,z+1/21
crystal symmetry operation4_556-x,-y,z+3/21
crystal symmetry operation4_557-x,-y,z+5/21
crystal symmetry operation4_558-x,-y,z+7/21
crystal symmetry operation4_559-x,-y,z+9/21
crystal symmetry operation4_551-x,-y,z-7/21
crystal symmetry operation4_552-x,-y,z-5/21
crystal symmetry operation4_553-x,-y,z-3/21
crystal symmetry operation4_554-x,-y,z-1/21
crystal symmetry operation5_555y,-x+y,z+1/61
crystal symmetry operation5_556y,-x+y,z+7/61
crystal symmetry operation5_557y,-x+y,z+13/61
crystal symmetry operation5_558y,-x+y,z+19/61
crystal symmetry operation5_559y,-x+y,z+25/61
crystal symmetry operation5_551y,-x+y,z-23/61
crystal symmetry operation5_552y,-x+y,z-17/61
crystal symmetry operation5_553y,-x+y,z-11/61
crystal symmetry operation5_554y,-x+y,z-5/61
crystal symmetry operation6_555x-y,x,z+5/61
crystal symmetry operation6_556x-y,x,z+11/61
crystal symmetry operation6_557x-y,x,z+17/61
crystal symmetry operation6_559x-y,x,z+29/61
crystal symmetry operation6_554x-y,x,z-1/61
Unit cell
Length a, b, c (Å)35.791, 35.791, 9.632
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide Psm alpha-3


Mass: 831.054 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 9 molecules

#2: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: 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: 2.14 Å3/Da / Density % sol: 42.6 % / Description: Needle-like
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Reservoir contained 0.2M potassium thiocyanate, 20% Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.5→100 Å / Num. obs: 1179 / % possible obs: 97.4 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.034 / Rrim(I) all: 0.131 / Χ2: 1.168 / Net I/σ(I): 5.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.559.60.7871180.8710.2580.8311.03498.3
1.55-1.6210.40.7491060.910.2420.791.11790.6
1.62-1.6911.50.6451160.880.1970.6761.09499.1
1.69-1.7811.60.471110.9210.1410.4921.10298.2
1.78-1.8914.80.2831210.980.0730.2931.2199.2
1.89-2.0415.50.2151080.990.0570.2231.15294.7
2.04-2.2415.70.1581230.9970.040.1631.15398.4
2.24-2.5615.90.1391160.9970.0360.1441.15697.5
2.56-3.2317.20.0981280.9980.0250.1011.05499.2
3.23-10015.10.0631320.9990.0170.0661.48798.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.51 Å31 Å
Translation1.51 Å31 Å

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Processing

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

Resolution: 1.51→31 Å / Cor.coef. Fo:Fc: 0.989 / Cor.coef. Fo:Fc free: 0.972 / SU B: 3.636 / SU ML: 0.051 / SU R Cruickshank DPI: 0.1142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.073
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1623 121 10.3 %RANDOM
Rwork0.1176 ---
obs0.1224 1057 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 67.74 Å2 / Biso mean: 13.433 Å2 / Biso min: 6.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: final / Resolution: 1.51→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms60 0 21 5 86
Biso mean--24.28 49.92 -
Num. residues----6
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0279
X-RAY DIFFRACTIONr_bond_other_d0.0040.0283
X-RAY DIFFRACTIONr_angle_refined_deg1.9952.1495
X-RAY DIFFRACTIONr_angle_other_deg1.1433192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.62355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.639203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.1581513
X-RAY DIFFRACTIONr_chiral_restr0.0840.27
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0264
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0220
X-RAY DIFFRACTIONr_rigid_bond_restr2.0573162
X-RAY DIFFRACTIONr_sphericity_free51
X-RAY DIFFRACTIONr_sphericity_bonded9.7465168
LS refinement shellResolution: 1.514→1.553 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 12 -
Rwork0.277 77 -
all-89 -
obs--98.89 %

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