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- PDB-6gq5: Crystal Structure of the PSMalpha3 Peptide Mutant L15A Forming Cr... -

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Basic information

Entry
Database: PDB / ID: 6gq5
TitleCrystal Structure of the PSMalpha3 Peptide Mutant L15A 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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 1.1Dec 25, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
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
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)2,6872
Polymers2,5691
Non-polymers1181
Water19811
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)48,37036
Polymers46,24318
Non-polymers2,12718
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,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 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 operation2_414-x-1,y-7/2,-z-11
crystal symmetry operation2_424-x-1,y-5/2,-z-11
crystal symmetry operation2_434-x-1,y-3/2,-z-11
crystal symmetry operation2_444-x-1,y-1/2,-z-11
crystal symmetry operation2_454-x-1,y+1/2,-z-11
crystal symmetry operation2_464-x-1,y+3/2,-z-11
crystal symmetry operation2_474-x-1,y+5/2,-z-11
crystal symmetry operation2_484-x-1,y+7/2,-z-11
crystal symmetry operation2_494-x-1,y+9/2,-z-11
Unit cell
Length a, b, c (Å)28.410, 10.670, 29.600
Angle α, β, γ (deg.)90.000, 105.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 2569.069 Da / Num. of mol.: 1 / Fragment: PSMalpha3 full-length mutant (residues 1-22) / Mutation: L15A / Source method: obtained synthetically / Details: PSMalpha3 L15A mutant, synthesized / Source: (synth.) Staphylococcus aureus RF122 / References: UniProt: P0C807
#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 1.68 Å3/Da / Density % sol: 26.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Reservoir contained 0.1 M CAPS pH 10.5, 40% 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: 1.5→17.47 Å / Num. obs: 2854 / % possible obs: 96.3 % / Redundancy: 2.68 % / Biso Wilson estimate: 20.678 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.137 / Rrim(I) all: 0.171 / Χ2: 0.957 / Net I/σ(I): 4.09
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.542.6520.5591.562070.8510.69295
1.54-1.582.5850.4761.682050.8410.60399
1.58-1.632.7510.4921.821810.8530.61197.8
1.63-1.682.7250.4672.082040.6820.59897.1
1.68-1.732.7580.3722.751900.7750.463100
1.73-1.792.7490.3512.641990.8860.43896.6
1.79-1.862.5950.3322.831580.8150.42499.4
1.86-1.942.7080.2543.421610.8960.31897
1.94-2.022.820.2184.111670.9150.26896
2.02-2.122.7090.1835.121580.9310.22597.5
2.12-2.242.5880.1585.251480.9370.19794.9
2.24-2.372.5230.1646.021320.9290.20692.3
2.37-2.542.3140.2015.541180.8980.24586.8
2.54-2.742.8530.1446.51290.9460.17697
2.74-32.7330.1246.661050.9750.15398.1
3-3.362.8770.1287.511140.9480.15896.6
3.36-3.872.5910.0877.38930.9920.10897.9
3.87-4.752.7230.0877.84830.980.1194.3
4.75-6.712.7540.0797.85610.9910.09793.8
6.71-17.472.2930.0446.99410.9980.05587.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRPacking: 0

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I55

5i55


Resolution: 1.5→17.47 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.272 / SU ML: 0.081 / SU R Cruickshank DPI: 0.1032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.108
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2449 286 10 %RANDOM
Rwork0.1943 ---
obs0.1995 2568 96.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 46.49 Å2 / Biso mean: 18.714 Å2 / Biso min: 8.73 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å20 Å20.94 Å2
2---0.3 Å20 Å2
3----1.93 Å2
Refinement stepCycle: final / Resolution: 1.5→17.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms182 0 8 11 201
Biso mean--41.26 23.33 -
Num. residues----22
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02193
X-RAY DIFFRACTIONr_bond_other_d0.0490.02197
X-RAY DIFFRACTIONr_angle_refined_deg1.6922.005255
X-RAY DIFFRACTIONr_angle_other_deg2.6713452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.581521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.48824.4449
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0941536
X-RAY DIFFRACTIONr_chiral_restr0.0960.226
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02202
X-RAY DIFFRACTIONr_gen_planes_other0.0230.0246
LS refinement shellResolution: 1.5→1.676 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.361 79 -
Rwork0.334 713 -
all-792 -
obs--97.42 %

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