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- PDB-6fg4: Crystal Structure of the Amyloid-like IIKVIK Segment from the S. ... -

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Basic information

Entry
Database: PDB / ID: 6fg4
TitleCrystal Structure of the Amyloid-like IIKVIK Segment from the S. aureus Biofilm-associated PSMalpha1
ComponentsPhenol-soluble modulin alpha 1 peptide
KeywordsPROTEIN FIBRIL / steric-zipper / cross-beta / 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-1
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 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
-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 9, 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 1.2Dec 25, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Mar 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 1.4May 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: Phenol-soluble modulin alpha 1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9073
Polymers7151
Non-polymers1922
Water362
1
A: Phenol-soluble modulin alpha 1 peptide
hetero molecules

A: Phenol-soluble modulin alpha 1 peptide
hetero molecules

A: Phenol-soluble modulin alpha 1 peptide
hetero molecules

A: Phenol-soluble modulin alpha 1 peptide
hetero molecules

A: Phenol-soluble modulin alpha 1 peptide
hetero molecules

A: Phenol-soluble modulin alpha 1 peptide
hetero molecules

A: Phenol-soluble modulin alpha 1 peptide
hetero molecules

A: Phenol-soluble modulin alpha 1 peptide
hetero molecules

A: Phenol-soluble modulin alpha 1 peptide
hetero molecules

A: Phenol-soluble modulin alpha 1 peptide
hetero molecules

A: Phenol-soluble modulin alpha 1 peptide
hetero molecules

A: Phenol-soluble modulin alpha 1 peptide
hetero molecules

A: Phenol-soluble modulin alpha 1 peptide
hetero molecules

A: Phenol-soluble modulin alpha 1 peptide
hetero molecules

A: Phenol-soluble modulin alpha 1 peptide
hetero molecules

A: Phenol-soluble modulin alpha 1 peptide
hetero molecules

A: Phenol-soluble modulin alpha 1 peptide
hetero molecules

A: Phenol-soluble modulin alpha 1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,32854
Polymers12,87018
Non-polymers3,45836
Water32418
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_555-x+1/2,y+1/2,-z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
crystal symmetry operation4_535-x+1/2,y-3/2,-z1
crystal symmetry operation4_525-x+1/2,y-5/2,-z1
crystal symmetry operation4_515-x+1/2,y-7/2,-z1
crystal symmetry operation4_565-x+1/2,y+3/2,-z1
crystal symmetry operation4_575-x+1/2,y+5/2,-z1
crystal symmetry operation4_585-x+1/2,y+7/2,-z1
crystal symmetry operation4_595-x+1/2,y+9/2,-z1
Unit cell
Length a, b, c (Å)45.270, 4.800, 22.900
Angle α, β, γ (deg.)90.000, 107.650, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-101-

SO4

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Components

#1: Protein/peptide Phenol-soluble modulin alpha 1 peptide / Psm alpha-1


Mass: 714.979 Da / Num. of mol.: 1
Fragment: Amyloid spine segment IIKVIK from PSMalpha1 (residues 7-12) secreted by S. aureus
Source method: obtained synthetically / Details: IIKVIK from PSMalpha1, synthesized / Source: (synth.) Staphylococcus aureus (bacteria) / References: UniProt: H9BRQ5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 1.66 Å3/Da / Density % sol: 25.82 % / Description: Needle like
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Reservoir contained 15% Polyethylene glycol 8,000: 0.5M Lithium sulfate

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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: Oct 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.1→18.38 Å / Num. obs: 2070 / % possible obs: 93.9 % / Redundancy: 11.161 % / Biso Wilson estimate: 10.349 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.133 / Rrim(I) all: 0.14 / Χ2: 0.919 / Net I/σ(I): 10.13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.1-1.136.4410.7522.141360.9670.82480
1.13-1.167.4130.9281.971260.9291.00680.8
1.16-1.198.030.8742.311320.8960.94280
1.19-1.2310.3910.9062.61280.9030.95894.8
1.23-1.2710.4680.4734.591260.9510.498100
1.27-1.3112.6420.4145.481230.9810.432100
1.31-1.3612.5150.4545.61320.9670.47399.2
1.36-1.4213.1690.4365.811300.9750.45497.7
1.42-1.4812.6380.4245.681270.9580.443100
1.48-1.5610.9350.2897.691240.9740.30396.1
1.56-1.6412.1460.20610.95960.9870.21684.2
1.64-1.7413.3510.211.71940.9880.20898.9
1.74-1.8613.7710.15112.27960.9970.157100
1.86-2.0113.0540.10718.37920.9990.112100
2.01-2.212.6840.09820.38980.9970.102100
2.2-2.4612.3850.08423.5910.9990.08894.8
2.46-2.84120.07524.41650.9990.0898.5
2.84-3.4810.8410.07426.81630.9960.079100
3.48-4.9211.0330.05635.52610.9990.058100
4.92-18.388.50.0725.763010.07593.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO / Packing: 0

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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 poly-ala beta-strand

Resolution: 1.1→18.38 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.313 / SU ML: 0.029 / SU R Cruickshank DPI: 0.0475 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.046
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1938 207 10 %RANDOM
Rwork0.1593 ---
obs0.1629 1863 94.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 35.35 Å2 / Biso mean: 9.926 Å2 / Biso min: 5.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20.2 Å2
2--0.05 Å2-0 Å2
3---0.07 Å2
Refinement stepCycle: final / Resolution: 1.1→18.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms50 0 10 2 62
Biso mean--14.62 33.63 -
Num. residues----6
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0273
X-RAY DIFFRACTIONr_bond_other_d0.0020.0293
X-RAY DIFFRACTIONr_angle_refined_deg1.9732.24898
X-RAY DIFFRACTIONr_angle_other_deg0.6993218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.34357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.2731521
X-RAY DIFFRACTIONr_chiral_restr0.1130.215
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0254
X-RAY DIFFRACTIONr_gen_planes_other00.026
X-RAY DIFFRACTIONr_rigid_bond_restr5.6743166
X-RAY DIFFRACTIONr_sphericity_free29.31351
X-RAY DIFFRACTIONr_sphericity_bonded2.145169
LS refinement shellResolution: 1.1→1.23 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.264 52 -
Rwork0.212 469 -
all-521 -
obs--83.49 %

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