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- PDB-6myj: Pleurotus ostreatus OstreolysinA plus sphingomyelin -

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Basic information

Entry
Database: PDB / ID: 6myj
TitlePleurotus ostreatus OstreolysinA plus sphingomyelin
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 / N-[(2S)-1-hydroxypropan-2-yl]butanamide / Ostreolysin A6
Function and homology information
Biological speciesPleurotus ostreatus (oyster mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 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 1.3Oct 11, 2023Group: 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

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)62,02129
Polymers60,5434
Non-polymers1,47925
Water9,872548
1
A: 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
2
B: Ostreolysin A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5318
Polymers15,1361
Non-polymers3957
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ostreolysin A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5318
Polymers15,1361
Non-polymers3957
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ostreolysin A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5527
Polymers15,1361
Non-polymers4166
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.425, 100.565, 58.813
Angle α, β, γ (deg.)90.000, 106.290, 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.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-K6V / N-[(2S)-1-hydroxypropan-2-yl]butanamide


Mass: 145.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 43.49 % / Mosaicity: 0.188 °
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, saturated sphingomyelin, saturated cholesterol, 30% 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: Nov 10, 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: 1.33→50 Å / Num. obs: 117866 / % possible obs: 99.4 % / Redundancy: 7.5 % / Biso Wilson estimate: 13.49 Å2 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.018 / Rrim(I) all: 0.049 / Χ2: 1.013 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.33-1.357.20.42958780.9060.170.4621.02599.7
1.35-1.387.50.38358820.9270.1490.4121.03999.7
1.38-1.47.50.32859080.9430.1270.3521.04599.5
1.4-1.437.40.29958440.9530.1160.3221.05599.5
1.43-1.467.30.26258400.9650.1030.2821.05299.3
1.46-1.56.80.22359030.9690.0910.2411.07599
1.5-1.547.50.18658860.9830.0720.21.08199.6
1.54-1.587.70.1658590.9880.0610.1721.06999.5
1.58-1.627.60.13658950.990.0520.1461.06699.6
1.62-1.687.50.12659180.9910.0490.1351.06999.5
1.68-1.747.30.10958500.9920.0430.1181.08499
1.74-1.8170.09158530.9940.0370.0981.04699.1
1.81-1.897.80.07758960.9960.0290.0831.05799.7
1.89-1.997.80.06359240.9970.0240.0681.05599.6
1.99-2.117.70.05358960.9980.020.0571.00699.4
2.11-2.277.10.04758570.9980.0190.0510.96499
2.27-2.580.04259140.9990.0160.0450.91399.9
2.5-2.877.90.03859410.9990.0150.0410.88499.7
2.87-3.617.40.03259180.9990.0120.0340.88499.1
3.61-507.70.02860040.9990.0110.030.82899.5

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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: MOLECULAR REPLACEMENT
Starting model: 4OV8
Resolution: 1.33→44.561 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 16.67
RfactorNum. reflection% reflection
Rfree0.1675 2000 1.7 %
Rwork0.1546 --
obs0.1548 117716 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 129.46 Å2 / Biso mean: 22.0634 Å2 / Biso min: 7.36 Å2
Refinement stepCycle: final / Resolution: 1.33→44.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4171 0 229 548 4948
Biso mean--37.6 26.95 -
Num. residues----541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164443
X-RAY DIFFRACTIONf_angle_d0.9495996
X-RAY DIFFRACTIONf_chiral_restr0.085649
X-RAY DIFFRACTIONf_plane_restr0.005765
X-RAY DIFFRACTIONf_dihedral_angle_d11.8141596
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3295-1.36280.22751400.20758086822697
1.3628-1.39960.25751420.19498278842099
1.3996-1.44080.20961440.185682478391100
1.4408-1.48730.18031420.17448233837599
1.4873-1.54050.18911420.16638255839799
1.5405-1.60220.18511440.155182848428100
1.6022-1.67510.16131420.151682808422100
1.6751-1.76340.17161430.15128212835599
1.7634-1.87390.16211430.150582918434100
1.8739-2.01860.14951430.142683068449100
2.0186-2.22170.1651430.14118245838899
2.2217-2.54320.15161430.14183038446100
2.5432-3.2040.1681440.15518296844099
3.204-44.58560.16111450.15768400854599
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.88270.5349-0.2191.6550.44450.89560.0607-0.0693-0.0877-0.0583-0.07130.04390.0445-0.1116-0.03530.115-0.0016-0.02140.0970.00440.0978-28.45035.89962.1006
28.8384-1.0537-2.44892.0835-1.37053.0225-0.0720.0647-0.0561-0.136-0.0474-0.14770.49030.38940.06470.16530.03970.0260.12540.01980.1675-17.1106-2.84865.0811
31.3049-0.62921.43481.6661-0.27332.8889-0.0205-0.1059-0.02450.08650.01590.11780.2695-0.19190.00290.1216-0.02130.01880.11010.00460.1216-30.3407-0.02847.0309
42.05090.3756-0.06611.91190.08621.6165-0.06820.0284-0.1659-0.0949-0.0528-0.05830.07450.11330.01290.10450.0060.00360.07660.00640.1049-22.79132.232-0.4498
53.943-1.73954.11131.5853-2.23665.857-0.05790.08990.01540.0022-0.2011-0.4964-0.09540.64380.13770.1371-0.0249-0.02690.23170.06480.2186-11.77328.51560.5145
61.55530.10390.95481.9891-0.11572.5948-0.11980.11160.0834-0.1387-0.03060.0133-0.22680.10150.15510.1761-0.0139-0.02580.11150.01760.1244-26.061313.192-3.1039
73.64231.1583-1.26393.01360.98171.25450.1531-0.1767-0.15610.49990.0928-0.1175-0.0836-0.1144-0.29310.158-0.0046-0.00040.11190.03280.1047-31.68036.853335.1673
80.725-0.4343-0.28450.9249-0.46261.51020.02820.05850.01920.0060.08620.10550.2078-0.1489-0.07140.1-0.0244-0.00230.11940.02880.1349-34.6817-0.681431.5649
91.3246-0.77380.64561.5888-0.15391.31550.0365-0.0152-0.11980.10840.19570.29590.1501-0.3962-0.18280.1435-0.03120.0250.21730.0830.183-40.09031.104431.0929
100.6927-0.0429-0.57570.00250.03540.47840.0008-0.8342-0.37260.4220.1461-0.21730.1589-0.08040.1070.4920.0531-0.23360.30220.03920.3217-18.6153-2.195240.8173
110.9790.0085-0.02951.5698-0.54441.79090.05080.0196-0.03330.02840.026-0.0220.0878-0.0342-0.06590.0904-0.0055-0.00260.09410.00640.0929-30.56615.881522.6135
124.3226-4.08923.16764.6574-3.81653.5152-0.1153-0.01610.310.7401-0.0764-0.7344-0.17220.45810.04830.2488-0.0416-0.0830.16360.00050.1985-22.482913.427533.583
132.51440.09062.15361.61820.06143.030.03550.05740.02290.12580.12020.1958-0.2604-0.3286-0.03620.10350.03340.0430.17390.05160.1293-38.727911.779124.4857
142.0459-0.0764-0.37611.10560.08271.2595-0.0495-0.17990.01710.27570.0517-0.03410.14380.0687-0.01590.21390.0114-0.01790.1273-0.00620.0971-22.4069-24.494714.6232
152.93312.4908-0.86592.3861-0.32620.8721-0.0070.02670.5730.06940.00310.07-0.2076-0.12520.01340.21650.02860.00570.1435-0.01590.1226-28.6234-14.39418.0628
160.1056-0.24150.4272.285-1.21713.13130.1611-0.0577-0.00910.2316-0.07790.1891-0.1721-0.2784-0.02780.25920.01130.04140.18750.00410.1263-34.873-16.42720.727
174.1766-2.7124-0.04953.6935-0.42620.9393-0.0492-0.51990.21040.23890.312-0.2490.04350.1507-0.19520.23290.0133-0.03460.1607-0.03120.1009-19.1558-15.445716.5958
188.4983-0.52550.68350.94470.18491.92580.1027-0.16340.04390.31060.0102-0.07450.10430.0275-0.12550.23260.0041-0.00510.11220.00690.1082-27.328-21.085918.0255
190.00310.05060.03890.83090.63830.4903-0.01-0.46620.72180.2853-0.09370.7792-0.6855-0.9168-0.0250.29790.06790.08260.576-0.0890.3681-45.2395-17.023114.4537
200.90350.00290.04181.03560.26211.0183-0.01680.0084-0.01140.0870.026-0.0751-0.0311-0.0226-0.01720.13960.00540.00560.0981-0.00370.0989-23.2397-19.4045.1181
211.4355-0.5027-0.34891.29880.20981.3196-0.07280.0463-0.16450.16880.01050.05270.1349-0.06980.0520.18580.0018-00.1102-0.01430.1089-25.893-28.53017.1253
222.22911.01990.54710.7460.2521.02790.03550.2458-0.3098-0.06250.0049-0.02110.03450.0106-0.01320.0726-0.00540.00870.0850.01260.1071-27.549124.455812.7308
237.85-3.4090.55151.8448-0.64120.8471-0.0343-0.00170.62210.09840.0032-0.0913-0.18770.0690.06720.0872-0.00860.00630.09360.00620.1089-25.480635.036619.6719
241.16871.25570.15171.99661.91775.48480.09160.17540.0229-0.43320.264-0.6008-0.33780.5211-0.17040.1574-0.02960.06970.146-0.03560.1751-17.396633.72458.4362
252.12630.6093-0.38711.23310.26910.6478-0.05020.12410.018-0.08860.09090.0437-0.0963-0.0488-0.03370.1025-0.0020.00050.11240.01160.0886-30.960231.580210.1738
263.0907-0.5052-2.19320.6760.18663.16460.0140.3211.0433-0.0908-0.0801-0.1332-0.23530.1572-0.36140.0997-0.01450.0130.25580.04940.3947-6.90731.82515.561
271.6963-0.13190.40341.1063-0.07230.6252-0.0142-0.1090.09120.11530.00230.0638-0.0526-0.03740.01480.07390.00730.02070.09130.00020.1031-30.847930.012122.2306
281.85811.251-2.06551.1241-1.35352.61190.0121-0.4358-0.41370.0999-0.1949-0.2812-0.0240.34010.06610.060.0013-0.00130.13410.02810.173-16.498821.826522.7238
292.06620.308-0.73431.2834-0.27011.14230.023-0.1659-0.11460.0603-0.0191-0.03960.03370.0258-0.00210.07820.00320.00420.10230.02120.0991-29.45919.592320.6764
302.8606-1.18250.75872.00520.56090.7072-0.1413-0.1061-0.33610.1210.0410.26540.1263-0.14940.110.0916-0.00430.02730.11490.02810.1338-36.607921.308817.1906
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 24 )A3 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 32 )A25 - 32
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 55 )A33 - 55
4X-RAY DIFFRACTION4chain 'A' and (resid 56 through 94 )A56 - 94
5X-RAY DIFFRACTION5chain 'A' and (resid 95 through 106 )A95 - 106
6X-RAY DIFFRACTION6chain 'A' and (resid 107 through 137 )A107 - 137
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 13 )B3 - 13
8X-RAY DIFFRACTION8chain 'B' and (resid 14 through 42 )B14 - 42
9X-RAY DIFFRACTION9chain 'B' and (resid 43 through 62 )B43 - 62
10X-RAY DIFFRACTION10chain 'B' and (resid 63 through 70 )B63 - 70
11X-RAY DIFFRACTION11chain 'B' and (resid 71 through 117 )B71 - 117
12X-RAY DIFFRACTION12chain 'B' and (resid 118 through 126 )B118 - 126
13X-RAY DIFFRACTION13chain 'B' and (resid 127 through 136 )B127 - 136
14X-RAY DIFFRACTION14chain 'C' and (resid 4 through 19 )C4 - 19
15X-RAY DIFFRACTION15chain 'C' and (resid 20 through 28 )C20 - 28
16X-RAY DIFFRACTION16chain 'C' and (resid 29 through 42 )C29 - 42
17X-RAY DIFFRACTION17chain 'C' and (resid 43 through 55 )C43 - 55
18X-RAY DIFFRACTION18chain 'C' and (resid 56 through 62 )C56 - 62
19X-RAY DIFFRACTION19chain 'C' and (resid 63 through 70 )C63 - 70
20X-RAY DIFFRACTION20chain 'C' and (resid 71 through 94 )C71 - 94
21X-RAY DIFFRACTION21chain 'C' and (resid 95 through 138 )C95 - 138
22X-RAY DIFFRACTION22chain 'D' and (resid 2 through 19 )D2 - 19
23X-RAY DIFFRACTION23chain 'D' and (resid 20 through 28 )D20 - 28
24X-RAY DIFFRACTION24chain 'D' and (resid 29 through 42 )D29 - 42
25X-RAY DIFFRACTION25chain 'D' and (resid 43 through 62 )D43 - 62
26X-RAY DIFFRACTION26chain 'D' and (resid 63 through 70 )D63 - 70
27X-RAY DIFFRACTION27chain 'D' and (resid 71 through 94 )D71 - 94
28X-RAY DIFFRACTION28chain 'D' and (resid 95 through 106 )D95 - 106
29X-RAY DIFFRACTION29chain 'D' and (resid 107 through 126 )D107 - 126
30X-RAY DIFFRACTION30chain 'D' and (resid 127 through 138 )D127 - 138

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