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- PDB-5i55: Crystal Structure of the Virulent PSM-alpha3 Peptide Forming a Cr... -

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Basic information

Entry
Database: PDB / ID: 5i55
TitleCrystal Structure of the Virulent PSM-alpha3 Peptide Forming a Cross-alpha amyloid-like Fibril
ComponentsPsm alpha-3
KeywordsPROTEIN FIBRIL / THE CROSS-ALPHA AMYLOID-LIKE FOLD IS COMPOSED OF MATING ALPHA-HELICAL SHEETS
Function / homology: / Phenol-soluble modulin alpha peptide / Phenol-soluble modulin alpha peptide family / killing of cells of another organism / ACETATE ION / Phenol-soluble modulin alpha 3 peptide / Phenol-soluble modulin alpha 3 peptide
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.45 Å
Model detailsPhenol Soluble Modulin
AuthorsLandau, M. / Moshe, A. / Tayeb-Fligelman, E. / Sawaya, M.R. / Coquelle, N. / Colletier, J.-P.
Funding support United States, Israel, 3items
OrganizationGrant numberCountry
United States - Israel Binational Science Foundation (BSF)2013254 United States
I-CORE Program of the Planning and Budgeting Committee and The Israel Science Foundation, Center of Excellence in Integrated Structural Cell Biology1775/12 Israel
the Support for training and career development of researchers (Marie Curie) CIG, Seventh framework program (FP7) of the European Commission, Single Beneficiary334260 Israel
CitationJournal: Science / Year: 2017
Title: The cytotoxic Staphylococcus aureus PSM alpha 3 reveals a cross-alpha amyloid-like fibril.
Authors: Tayeb-Fligelman, E. / Tabachnikov, O. / Moshe, A. / Goldshmidt-Tran, O. / Sawaya, M.R. / Coquelle, N. / Colletier, J.P. / Landau, M.
History
DepositionFeb 14, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
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 1.3Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)2,8353
Polymers2,6581
Non-polymers1772
Water21612
1
A: Psm alpha-3
hetero molecules
x 20


Theoretical massNumber of molelcules
Total (without water)56,70560
Polymers53,16120
Non-polymers3,54440
Water36020
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_655x+1,y,z1
crystal symmetry operation1_665x+1,y+1,z1
crystal symmetry operation1_675x+1,y+2,z1
crystal symmetry operation1_685x+1,y+3,z1
crystal symmetry operation1_695x+1,y+4,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
crystal symmetry operation2_666-x+1,y+3/2,-z+11
crystal symmetry operation2_676-x+1,y+5/2,-z+11
crystal symmetry operation2_686-x+1,y+7/2,-z+11
crystal symmetry operation2_696-x+1,y+9/2,-z+11
crystal symmetry operation2_756-x+2,y+1/2,-z+11
crystal symmetry operation2_766-x+2,y+3/2,-z+11
crystal symmetry operation2_776-x+2,y+5/2,-z+11
crystal symmetry operation2_786-x+2,y+7/2,-z+11
crystal symmetry operation2_796-x+2,y+9/2,-z+11
Unit cell
Length a, b, c (Å)29.460, 10.510, 29.710
Angle α, β, γ (deg.)90.000, 111.980, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Psm alpha-3


Mass: 2658.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PSM-alpha3 from S. aureus, synthesized / Source: (synth.) Staphylococcus aureus (bacteria) / References: UniProt: H9BRQ7, UniProt: P0C805*PLUS
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.61 Å3/Da / Density % sol: 23.48 % / Description: Needle-shaped microcrystal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: reservoir contained 0.2 M ammonium acetate, 0.1M BisTris pH 5.5, 45% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792,0.9794,0.9796
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 18, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97941
30.97961
ReflectionResolution: 1.45→16.55 Å / Num. obs: 3126 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 18.97 % / Biso Wilson estimate: 18.998 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.13 / Χ2: 1.019 / Net I/σ(I): 10.01 / Num. measured all: 59309
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.45-1.4919.30.4583.7843514694110.990.48287.6
1.49-1.530.5413.740013903730.9710.56895.6
1.53-1.570.4594.0840464154060.9790.48497.8
1.57-1.620.4484.4637933813730.9680.47297.9
1.62-1.670.3535.3141933953880.9860.3798.2
1.67-1.730.3216.1142104113940.9870.33795.9
1.73-1.80.3246.2632863333110.9840.34193.4
1.8-1.870.258.0937063373340.990.26299.1
1.87-1.960.2038.6135593443420.9950.21399.4
1.96-2.050.19710.0832743313250.990.20898.2
2.05-2.160.16710.7625923092890.9850.17793.5
2.16-2.290.14513.7726072632520.9930.15295.8
2.29-2.450.1315.7729742722720.9950.136100
2.45-2.650.11317.1426892682660.9950.11899.3
2.65-2.90.10418.6522942202140.9960.10997.3
2.9-3.240.09420.7222352032030.9950.099100
3.24-3.740.08421.2218571881830.9960.08897.3
3.74-4.590.07224.2114911561340.9970.07585.9
4.59-6.480.0723.413881231200.9980.07397.6
6.480.06222.94763676410.06595.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.45→16.55 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.1785 / WRfactor Rwork: 0.1412 / FOM work R set: 0.8277 / SU B: 1.744 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0727 / SU Rfree: 0.0777 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1837 313 10 %RANDOM
Rwork0.1427 ---
obs0.1466 2812 96.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.03 Å2 / Biso mean: 16.958 Å2 / Biso min: 10.85 Å2
Baniso -1Baniso -2Baniso -3
1--2.18 Å2-0 Å20.12 Å2
2---1.07 Å20 Å2
3---2.41 Å2
Refinement stepCycle: final / Resolution: 1.45→16.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms185 0 12 12 209
Biso mean--19.19 25.92 -
Num. residues----22
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02209
X-RAY DIFFRACTIONr_bond_other_d0.0020.02223
X-RAY DIFFRACTIONr_angle_refined_deg1.9962.05276
X-RAY DIFFRACTIONr_angle_other_deg0.9743510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.467523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.30424.4449
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3641539
X-RAY DIFFRACTIONr_chiral_restr0.1480.228
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02224
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0252
LS refinement shellResolution: 1.45→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 23 -
Rwork0.225 201 -
all-224 -
obs--90.32 %

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