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- PDB-6myk: Pleurotus ostreatus OstreolysinA mutant E69A with Bis-Tris -

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Basic information

Entry
Database: PDB / ID: 6myk
TitlePleurotus ostreatus OstreolysinA mutant E69A with Bis-Tris
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 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 ...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 / 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)61,26421
Polymers60,0824
Non-polymers1,18217
Water9,062503
1
A: Ostreolysin A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4508
Polymers15,0211
Non-polymers4297
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ostreolysin A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1403
Polymers15,0211
Non-polymers1192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ostreolysin A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2645
Polymers15,0211
Non-polymers2434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ostreolysin A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4115
Polymers15,0211
Non-polymers3904
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.857, 86.684, 92.878
Angle α, β, γ (deg.)90.000, 99.130, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-351-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Ostreolysin A6


Mass: 15020.611 Da / Num. of mol.: 4 / Mutation: C62S, E69A, 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

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Non-polymers , 5 types, 520 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 2.3 Å3/Da / Density % sol: 46.56 % / Mosaicity: 0.319 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris, 0.125 M lithium sulfate, 25% (w/v) PEG3350, 25% 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: 0.97903 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 19, 2017 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 47399 / % possible obs: 93.4 % / Redundancy: 5.2 % / Biso Wilson estimate: 18.08 Å2 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.018 / Rrim(I) all: 0.043 / Χ2: 0.986 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.833.90.43817010.8880.2330.4990.91768.4
1.83-1.864.10.40919860.9180.2150.4640.94777.8
1.86-1.94.30.36920680.9360.1890.4160.98183
1.9-1.944.40.33722120.9540.170.3791.00687.1
1.94-1.984.70.28722800.9660.1420.3220.95489.4
1.98-2.034.80.25523620.9760.1260.2860.9794.2
2.03-2.084.90.2324260.9820.1130.2571.01196
2.08-2.135.10.18524670.9870.090.2070.97397.5
2.13-2.24.90.15523840.9910.0770.1751.00294.3
2.2-2.275.70.13624980.9950.0630.151.03698.8
2.27-2.355.80.11925060.9950.0540.1310.99699
2.35-2.445.70.10525130.9950.0490.1160.98999.2
2.44-2.555.80.08524990.9980.0390.0930.99598.6
2.55-2.695.60.06625190.9980.0310.0731.02998.9
2.69-2.865.30.05223790.9980.0250.0581.02394.6
2.86-3.0860.04425380.9980.020.0481.02899
3.08-3.395.90.03424970.9990.0160.0381.04898.8
3.39-3.885.60.0325310.9990.0140.0331.05499
3.88-4.885.50.02624810.9990.0120.0290.95296.9
4.88-505.70.02425520.9990.0110.0270.74397.7

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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

4ov8


Resolution: 1.8→49.265 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.52
RfactorNum. reflection% reflection
Rfree0.219 1401 3.4 %
Rwork0.1944 --
obs0.1952 41217 81.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.7 Å2 / Biso mean: 26.877 Å2 / Biso min: 6.29 Å2
Refinement stepCycle: final / Resolution: 1.8→49.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4165 0 136 503 4804
Biso mean--39.46 29.08 -
Num. residues----542
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 (%)
1.8001-1.86450.3129750.25412136221144
1.8645-1.93910.2801960.23932708280456
1.9391-2.02740.25971130.23453212332566
2.0274-2.13430.26151280.22963635376375
2.1343-2.2680.24131440.22074090423484
2.268-2.44310.28361690.21474758492798
2.4431-2.68890.25541690.21194857502699
2.6889-3.0780.23311670.19764732489997
3.078-3.87770.18161700.16864845501599
3.8777-49.28290.17111700.16684843501397
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4095-0.01220.27360.2160.13250.28830.0890.025-0.10350.10220.0396-0.05860.1250.01240.02970.15470.00860.00070.03040.03290.1712-8.089221.576329.5032
22.66350.85632.15381.88671.34692.6180.0979-0.2441-0.34050.35710.0847-0.00560.4773-0.1141-0.1650.23860.0284-0.03850.12240.04010.1953-8.001610.828329.9964
33.31391.38310.27723.4205-0.63111.54280.0865-0.21330.24640.2276-0.04840.1604-0.24220.01640.01910.13830.00770.00480.05660.00630.1103-8.584127.938131.9625
40.2965-0.2895-0.16172.1868-0.17650.1470.06840.1208-0.0942-0.175-0.033-0.27350.14460.10170.02880.1490.0571-0.02110.0683-0.02710.1683-1.533717.328221.0037
51.68681.1541.5312.4323.56727.4184-0.12370.15940.5795-0.19350.03590.2625-0.81180.11750.0560.2673-0.04640.05690.12020.06050.2397-6.965239.162221.5722
61.8257-0.27530.02462.4433-0.0471.20740.12750.3192-0.112-0.3974-0.00660.09030.0944-0.1107-0.10290.13110.0136-0.02530.13520.02040.0931-9.662919.893816.0983
70.9983-0.01650.49421.0267-0.13031.23880.03480.27730.057-0.21160.04950.21170.0288-0.3445-0.07850.17360.0372-0.02260.41680.0230.1447-11.772825.5085-6.5134
82.1856-1.55652.25572.9701-2.40742.67240.32830.6997-0.1436-0.7155-0.31150.13880.47140.0253-0.04740.3146-0.0603-0.03680.5953-0.03220.2007-15.638615.5892-8.5072
92.48330.03210.92842.00531.16381.73620.110.11140.0892-0.1224-0.07750.16340.023-0.394-0.01560.11460.024-0.02960.41680.04780.1248-16.233725.7042-1.9543
105.71924.538-3.40918.5701-5.74586.09330.5235-0.07140.47540.6799-0.2990.5207-0.5412-0.1757-0.21140.15610.02940.04540.3462-0.00960.1229-14.181229.70246.3847
111.65680.3022-0.91242.982-1.73091.98720.17210.0174-0.19460.1313-0.11570.02210.1948-0.1227-0.05360.1685-0.0373-0.04860.27580.00340.1011-10.198119.62176.1522
121.3890.38130.05761.94490.14411.81750.06720.22410.3807-0.2741-0.00590.2477-0.0861-0.413-0.03560.17380.035-0.02580.22010.08860.2324-28.334831.633217.0109
133.34030.20890.13831.4053-0.38651.90240.06630.51850.1211-0.53570.02660.34880.1983-0.4708-0.08020.22750.0008-0.07850.29740.03430.1945-31.679425.795413.2342
142.4069-0.02280.7781.37771.122.39280.1404-0.19330.3797-0.1445-0.13620.0936-0.0229-0.57880.01780.12240.0229-0.00540.31370.05070.2229-34.369431.995922.8245
154.38553.2531-0.94977.631-0.36933.46250.4463-0.25390.41090.2383-0.12410.1232-0.1364-0.2889-0.26220.1526-0.00610.07780.31290.0510.1904-29.996431.552730.8157
160.6998-0.19450.06590.05920.04910.9190.237-0.0375-0.02710.0821-0.050.1740.2502-0.408-0.07080.1959-0.1308-0.04090.23710.08660.1812-27.545323.174327.0685
172.14610.64841.11721.3860.55410.62260.0477-0.2403-0.1802-0.08050.080.0420.237-0.2992-0.06130.2452-0.182-0.01830.38570.05170.2237-30.362214.596244.8132
181.1730.1685-0.75690.4812-0.23720.5481-0.013-0.1375-0.07820.18870.03990.1720.1644-0.3901-0.00470.2572-0.1413-0.00150.5850.11670.1808-26.957418.408756.8595
190.17270.0826-0.00760.2955-0.0008-0.0001-0.088-0.0175-0.2183-0.10940.0364-0.02970.1735-0.11280.01660.4174-0.29060.00880.51380.13480.3202-32.15799.74447.4834
201.25370.71810.02971.37-0.23390.48170.0142-0.07-0.23990.0256-0.0366-0.03540.2134-0.130.09640.2007-0.1103-0.02060.10250.06890.1541-22.534515.62944.6579
212.3034-0.542-0.80050.8482-1.2813.2734-0.1813-0.00810.0257-0.35890.255-0.2815-0.59460.0804-0.09870.1954-0.0487-0.00090.10230.03740.135-22.107923.426540.5471
223.5359-0.62760.14892.66141.97335.0646-0.15210.011-0.0605-0.35510.05940.3029-0.1564-0.53420.11220.1757-0.0959-0.04390.2890.08260.1267-30.893420.283337.5126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 42 )A2 - 42
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 55 )A43 - 55
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 70 )A56 - 70
4X-RAY DIFFRACTION4chain 'A' and (resid 71 through 94 )A71 - 94
5X-RAY DIFFRACTION5chain 'A' and (resid 95 through 101 )A95 - 101
6X-RAY DIFFRACTION6chain 'A' and (resid 102 through 136 )A102 - 136
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 42 )B2 - 42
8X-RAY DIFFRACTION8chain 'B' and (resid 43 through 55 )B43 - 55
9X-RAY DIFFRACTION9chain 'B' and (resid 56 through 94 )B56 - 94
10X-RAY DIFFRACTION10chain 'B' and (resid 95 through 111 )B95 - 111
11X-RAY DIFFRACTION11chain 'B' and (resid 112 through 138 )B112 - 138
12X-RAY DIFFRACTION12chain 'C' and (resid 2 through 42 )C2 - 42
13X-RAY DIFFRACTION13chain 'C' and (resid 43 through 62 )C43 - 62
14X-RAY DIFFRACTION14chain 'C' and (resid 63 through 94 )C63 - 94
15X-RAY DIFFRACTION15chain 'C' and (resid 95 through 111 )C95 - 111
16X-RAY DIFFRACTION16chain 'C' and (resid 112 through 136 )C112 - 136
17X-RAY DIFFRACTION17chain 'D' and (resid 2 through 24 )D2 - 24
18X-RAY DIFFRACTION18chain 'D' and (resid 25 through 42 )D25 - 42
19X-RAY DIFFRACTION19chain 'D' and (resid 43 through 62 )D43 - 62
20X-RAY DIFFRACTION20chain 'D' and (resid 63 through 94 )D63 - 94
21X-RAY DIFFRACTION21chain 'D' and (resid 95 through 111 )D95 - 111
22X-RAY DIFFRACTION22chain 'D' and (resid 112 through 136 )D112 - 136

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