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- PDB-6gqc: Crystal Structure of the PSMalpha3 Peptide Mutant G16A Forming Cr... -

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Basic information

Entry
Database: PDB / ID: 6gqc
TitleCrystal Structure of the PSMalpha3 Peptide Mutant G16A 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 subsp. aureus NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 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
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)2,7074
Polymers2,6251
Non-polymers813
Water362
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)48,71972
Polymers47,25318
Non-polymers1,46654
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_445-x-1/2,y-1/2,-z1
crystal symmetry operation4_455-x-1/2,y+1/2,-z1
crystal symmetry operation4_465-x-1/2,y+3/2,-z1
crystal symmetry operation4_475-x-1/2,y+5/2,-z1
crystal symmetry operation4_485-x-1/2,y+7/2,-z1
crystal symmetry operation4_495-x-1/2,y+9/2,-z1
crystal symmetry operation4_415-x-1/2,y-7/2,-z1
crystal symmetry operation4_425-x-1/2,y-5/2,-z1
crystal symmetry operation4_435-x-1/2,y-3/2,-z1
Unit cell
Length a, b, c (Å)53.270, 13.300, 25.800
Angle α, β, γ (deg.)90.000, 111.910, 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: 2625.176 Da / Num. of mol.: 1 / Fragment: PSMalpha3 full-lenght mutant (residues 1-22) / Mutation: G16A / Source method: obtained synthetically / Details: PSMalpha3 G16A mutant, synthesized
Source: (synth.) Staphylococcus aureus subsp. aureus NCTC 8325
References: UniProt: P0C805
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: 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: 1.62 Å3/Da / Density % sol: 23.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Reservoir contained 0.1 M sodium acetate pH 4.6, 0.01 M Cobalt chloride, 1.0 M 1,6-Hexanediol with cryo protection of 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.4→14.67 Å / Num. obs: 3478 / % possible obs: 99 % / Redundancy: 6.302 % / Biso Wilson estimate: 22.139 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.135 / Χ2: 0.884 / Net I/σ(I): 8.13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.4-1.446.1310.7542.282670.8490.822100
1.44-1.486.1150.692.672440.8210.75394.9
1.48-1.526.0830.4683.32420.9650.513100
1.52-1.576.5960.4184.142080.9570.455100
1.57-1.626.1840.414.292450.9360.44899.2
1.62-1.676.530.3335.292150.9640.36298.2
1.67-1.746.8570.2736.161960.970.29699.5
1.74-1.816.6370.237.082040.9750.25100
1.81-1.896.4140.1957.732030.9860.212100
1.89-1.986.4150.17991950.9760.19598.5
1.98-2.096.0630.13111.021750.9820.14499.4
2.09-2.216.4390.12612.11800.9870.13798.9
2.21-2.376.0530.12212.491500.9790.13498.7
2.37-2.566.5320.12213.861540.9840.132100
2.56-2.86.5450.11514.691340.9760.12698.5
2.8-3.136.450.10115.211310.9890.11100
3.13-3.625.7270.10514.881100.9880.11699.1
3.62-4.435.6830.09715.411040.9920.10799
4.43-6.266.040.08815.84750.9940.09798.7
6.26-14.675.370.10114.79460.9960.11490.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO / Packing: 1

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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: 1.4→14.67 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.559 / SU ML: 0.045 / SU R Cruickshank DPI: 0.0844 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.071
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1928 348 10 %RANDOM
Rwork0.1506 ---
obs0.1548 3129 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 53.66 Å2 / Biso mean: 18.28 Å2 / Biso min: 10.33 Å2
Baniso -1Baniso -2Baniso -3
1--1.54 Å20 Å2-0.22 Å2
2--0.95 Å20 Å2
3---0.58 Å2
Refinement stepCycle: final / Resolution: 1.4→14.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms186 0 3 2 191
Biso mean--46.79 24.65 -
Num. residues----22
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02199
X-RAY DIFFRACTIONr_bond_other_d0.0060.02203
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.989265
X-RAY DIFFRACTIONr_angle_other_deg0.913469
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.316523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88924.4449
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.5011540
X-RAY DIFFRACTIONr_chiral_restr0.0860.228
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02216
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0248
X-RAY DIFFRACTIONr_rigid_bond_restr6.7343402
X-RAY DIFFRACTIONr_sphericity_free13.69652
X-RAY DIFFRACTIONr_sphericity_bonded4.865400
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 26 -
Rwork0.239 238 -
all-264 -
obs--100 %

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