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- PDB-6gq2: Crystal Structure of the PSMalpha3 Peptide Mutant K12A Forming Cr... -

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Basic information

Entry
Database: PDB / ID: 6gq2
TitleCrystal Structure of the PSMalpha3 Peptide Mutant K12A Forming Cross-Alpha Amyloid-like Fibril
ComponentsPhenol-soluble modulin alpha 3 peptide
KeywordsPROTEIN FIBRIL / cross-alpha / fibril / amyloid / mating alpha-helical sheets
Function / homologyPhenol-soluble modulin alpha peptide / Phenol-soluble modulin alpha peptide family / killing of cells of another organism / Phenol-soluble modulin alpha 3 peptide
Function and homology information
Biological speciesStaphylococcus aureus RF122 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / molecular replacement / Resolution: 1.54 Å
Model detailsS. aureus
AuthorsLandau, M. / Tayeb-Fligelman, E.
CitationJournal: Structure / Year: 2020
Title: Staphylococcus aureus PSM alpha 3 Cross-alpha Fibril Polymorphism and Determinants of Cytotoxicity.
Authors: Tayeb-Fligelman, E. / Salinas, N. / Tabachnikov, O. / Landau, M.
History
DepositionJun 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Derived calculations / Category: pdbx_struct_assembly
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.2Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phenol-soluble modulin alpha 3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,6492
Polymers2,5531
Non-polymers961
Water543
1
A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules

A: Phenol-soluble modulin alpha 3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,68436
Polymers45,95518
Non-polymers1,72918
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_656-x+3/2,y+1/2,-z+11
crystal symmetry operation4_646-x+3/2,y-1/2,-z+11
crystal symmetry operation4_636-x+3/2,y-3/2,-z+11
crystal symmetry operation4_626-x+3/2,y-5/2,-z+11
crystal symmetry operation4_616-x+3/2,y-7/2,-z+11
crystal symmetry operation4_666-x+3/2,y+3/2,-z+11
crystal symmetry operation4_676-x+3/2,y+5/2,-z+11
crystal symmetry operation4_686-x+3/2,y+7/2,-z+11
crystal symmetry operation4_696-x+3/2,y+9/2,-z+11
Unit cell
Length a, b, c (Å)52.940, 13.150, 25.970
Angle α, β, γ (deg.)90.000, 112.260, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide Phenol-soluble modulin alpha 3 peptide


Mass: 2553.048 Da / Num. of mol.: 1 / Fragment: PSMalpha3 full-lenght mutant (residues 1-22) / Mutation: K12A / Source method: obtained synthetically / Details: PSMalpha3 K12A mutant, synthesized / Source: (synth.) Staphylococcus aureus RF122 / References: UniProt: P0C807
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 1.64 Å3/Da / Density % sol: 24.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Reservoir contained 0.1 M HEPES pH 7.5, 0.5 M Ammonium Sulfate, 30% v/v 2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Nov 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.54→14.61 Å / Num. obs: 2477 / % possible obs: 94.1 % / Redundancy: 2.77 % / Biso Wilson estimate: 24.837 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.114 / Rrim(I) all: 0.142 / Χ2: 0.921 / Net I/σ(I): 4.83
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.54-1.582.7210.8361.21720.7721.03291.5
1.58-1.622.6930.9051.081920.7521.11797.5
1.62-1.672.7930.5961.661640.8150.72397
1.67-1.722.9050.5361.851680.9070.65996.6
1.72-1.782.8550.5671.921650.7950.69598.2
1.78-1.842.780.3562.621730.9470.44496.6
1.84-1.912.7690.3532.731470.9290.43598
1.91-1.992.8460.3212.981490.9360.39799.3
1.99-2.072.7030.2114.821450.9540.26196
2.07-2.182.7940.2294.831360.9190.28295.1
2.18-2.292.5320.1446.181240.9680.17993.2
2.29-2.432.5320.1276.41090.9660.16183.8
2.43-2.62.5580.1167.411040.9820.14485.2
2.6-2.812.960.1018.971000.9770.12490.1
2.81-3.082.9410.0979.661010.9730.12294.4
3.08-3.442.9250.0811.16930.9830.09793
3.44-3.972.8960.05912.26770.9970.07291.7
3.97-4.862.6890.07211.86740.9710.09496.1
4.86-6.882.8910.05912.55550.9940.07288.7
6.88-14.612.5520.0811.54290.9930.09880.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.54→14.61 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 8.993 / SU ML: 0.119 / SU R Cruickshank DPI: 0.1975 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.112
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.236 248 10 %RANDOM
Rwork0.2034 ---
obs0.2067 2229 94.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 94.4 Å2 / Biso mean: 26.844 Å2 / Biso min: 15.24 Å2
Baniso -1Baniso -2Baniso -3
1--3.22 Å20 Å2-0.04 Å2
2---0.7 Å20 Å2
3---2.95 Å2
Refinement stepCycle: final / Resolution: 1.54→14.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms181 0 5 3 189
Biso mean--85.66 33.59 -
Num. residues----22
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02189
X-RAY DIFFRACTIONr_bond_other_d0.0060.02182
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.997251
X-RAY DIFFRACTIONr_angle_other_deg0.913419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.705521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.35524.4449
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4671534
X-RAY DIFFRACTIONr_chiral_restr0.0820.226
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02202
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0246
X-RAY DIFFRACTIONr_rigid_bond_restr2.2593367
X-RAY DIFFRACTIONr_sphericity_free10.96951
X-RAY DIFFRACTIONr_sphericity_bonded6.6335370
LS refinement shellResolution: 1.538→1.717 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.38 69 -
Rwork0.379 620 -
all-689 -
obs--96.23 %

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