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- PDB-6myi: Pleurotus ostreatus OstreolysinA -

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Basic information

Entry
Database: PDB / ID: 6myi
TitlePleurotus ostreatus OstreolysinA
ComponentsOstreolysin A6
KeywordsMEMBRANE PROTEIN / BETA-SANDWICH FOLD / MEMBRANE BINDING PROTEIN
Function / homologyMutm (Fpg) Protein; Chain: A, domain 2 - #50 / Hemolysin, aegerolysin type / Aegerolysin / Mutm (Fpg) Protein; Chain: A, domain 2 / hemolysis by symbiont of host erythrocytes / Sandwich / Mainly Beta / Ostreolysin A6
Function and homology information
Biological speciesPleurotus ostreatus (oyster mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.15 Å
AuthorsTomchick, D.R. / Radhakrishnan, A. / Endapally, S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL20948 United States
American Heart Association12SDG12040267 United States
Welch FoundationI-1793 United States
CitationJournal: Cell / Year: 2019
Title: Molecular Discrimination between Two Conformations of Sphingomyelin in Plasma Membranes.
Authors: Endapally, S. / Frias, D. / Grzemska, M. / Gay, A. / Tomchick, D.R. / Radhakrishnan, A.
History
DepositionNov 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ostreolysin A6
B: Ostreolysin A6
C: Ostreolysin A6
D: Ostreolysin A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,31819
Polymers60,5434
Non-polymers77515
Water11,223623
1
A: Ostreolysin A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3455
Polymers15,1361
Non-polymers2094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ostreolysin A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2834
Polymers15,1361
Non-polymers1473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ostreolysin A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4076
Polymers15,1361
Non-polymers2715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ostreolysin A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2834
Polymers15,1361
Non-polymers1473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.430, 100.335, 59.018
Angle α, β, γ (deg.)90.000, 106.430, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ostreolysin A6


Mass: 15135.701 Da / Num. of mol.: 4 / Mutation: C62S, C94S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pleurotus ostreatus (oyster mushroom) / Gene: OlyA6 / Plasmid: pLysS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P83467
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 623 / 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: 2.18 Å3/Da / Density % sol: 43.52 % / Mosaicity: 0.666 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M ammonium chloride, 0.05 M tris hydrochloride, 0.15 M sodium chloride, 19% (w/v) PEG3350, 30% (w/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 16, 2016 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 205258 / % possible obs: 97.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 15.15 Å2 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.019 / Rrim(I) all: 0.05 / Χ2: 0.954 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.1-1.124.40.91593470.6310.4491.0250.93589.6
1.12-1.144.60.80897750.6820.3970.9040.91893.3
1.14-1.165.60.754100810.7520.3320.8260.95596.2
1.16-1.186.10.677101820.8160.2880.7370.96197.1
1.18-1.216.30.584102260.8610.2470.6360.97997.8
1.21-1.246.20.511102280.8780.2190.5580.97597.9
1.24-1.2760.438102800.8960.1910.4790.96998
1.27-1.35.70.359102400.9260.1620.3960.97497.6
1.3-1.346.40.302102850.9530.1260.3280.99198.4
1.34-1.396.40.257103400.9630.1080.280.9798.7
1.39-1.446.40.208103750.9730.0870.2260.99598.9
1.44-1.496.40.164104040.9830.070.1791.01199
1.49-1.565.90.123102730.9880.0540.1351.03698.3
1.56-1.646.60.095104270.9940.040.1031.02299.1
1.64-1.756.80.077104250.9950.0320.0830.97199.5
1.75-1.886.70.062104720.9960.0250.0670.96399.6
1.88-2.076.50.05104470.9970.0210.0540.96999.4
2.07-2.376.50.043104140.9980.0180.0470.95798.8
2.37-2.997.10.036104850.9980.0150.0390.80899.5
2.99-506.80.031105520.9990.0130.0340.74899

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX(1.12_2829)refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MIR / Resolution: 1.15→33.305 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.03
RfactorNum. reflection% reflection
Rfree0.1606 1451 0.87 %
Rwork0.1417 --
obs0.1419 166128 90.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 64.24 Å2 / Biso mean: 21.0846 Å2 / Biso min: 9.59 Å2
Refinement stepCycle: final / Resolution: 1.15→33.305 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4197 0 48 623 4868
Biso mean--30.44 29.63 -
Num. residues----545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0184438
X-RAY DIFFRACTIONf_angle_d1.1546011
X-RAY DIFFRACTIONf_chiral_restr0.096655
X-RAY DIFFRACTIONf_plane_restr0.007768
X-RAY DIFFRACTIONf_dihedral_angle_d11.0231598
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.15-1.19110.2691660.20477433749941
1.1911-1.23880.18691250.168146281475381
1.2388-1.29520.17761480.1501167311687992
1.2952-1.36350.16751560.1386177671792398
1.3635-1.44890.13691590.1303179241808399
1.4489-1.56080.13741580.118178941805299
1.5608-1.71780.14441590.1195179901814999
1.7178-1.96640.15491600.12741808818248100
1.9664-2.47730.15571590.139180391819899
2.4773-33.3190.16881610.1535181831834499

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