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- PDB-7rrh: Crystal structure of fast switching R66M/M159T mutant of fluoresc... -

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Basic information

Entry
Database: PDB / ID: 7rrh
TitleCrystal structure of fast switching R66M/M159T mutant of fluorescent protein Dronpa (Dronpa2)
ComponentsFluorescent protein Dronpa
KeywordsFLUORESCENT PROTEIN / Dronpa2
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / identical protein binding / metal ion binding / Fluorescent protein Dronpa
Function and homology information
Biological speciesEchinophyllia sp. SC22 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.747 Å
AuthorsLin, C.-Y. / Romei, M.G. / Mathews, I.I. / Boxer, S.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118044 United States
National Science Foundation (NSF, United States)CHE-1740645 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Energetic Basis and Design of Enzyme Function Demonstrated Using GFP, an Excited-State Enzyme.
Authors: Lin, C.Y. / Romei, M.G. / Mathews, I.I. / Boxer, S.G.
History
DepositionAug 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fluorescent protein Dronpa
B: Fluorescent protein Dronpa
C: Fluorescent protein Dronpa
D: Fluorescent protein Dronpa
E: Fluorescent protein Dronpa
F: Fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)173,6136
Polymers173,6136
Non-polymers00
Water15,511861
1
A: Fluorescent protein Dronpa
F: Fluorescent protein Dronpa

A: Fluorescent protein Dronpa
F: Fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)115,7424
Polymers115,7424
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
2
B: Fluorescent protein Dronpa
C: Fluorescent protein Dronpa
D: Fluorescent protein Dronpa
E: Fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)115,7424
Polymers115,7424
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)186.629, 71.536, 108.271
Angle α, β, γ (deg.)90.00, 110.12, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-336-

HOH

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Components

#1: Protein
Fluorescent protein Dronpa


Mass: 28935.580 Da / Num. of mol.: 6 / Mutation: R66M/M159T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Echinophyllia sp. SC22 (invertebrata) / Gene: Dronpa / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5TLG6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 861 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.95 Å3/Da / Density % sol: 37.07 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.1 M Tris-HCl pH 7.4, 0.1 M MgCl2, 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.747→37.77 Å / Num. obs: 132790 / % possible obs: 98.2 % / Redundancy: 13.5 % / Biso Wilson estimate: 32.3 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.019 / Rrim(I) all: 0.071 / Net I/σ(I): 18.4
Reflection shellResolution: 1.747→1.813 Å / Redundancy: 12.8 % / Rmerge(I) obs: 1.85 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 12922 / CC1/2: 0.714 / CC star: 0.913 / Rpim(I) all: 0.53 / Rrim(I) all: 1.92 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX1.13rc2_2986refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UTS
Resolution: 1.747→37.768 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2022 6641 5 %
Rwork0.1764 --
obs0.1777 132790 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.747→37.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10344 0 0 861 11205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810907
X-RAY DIFFRACTIONf_angle_d1.32814762
X-RAY DIFFRACTIONf_dihedral_angle_d5.2778893
X-RAY DIFFRACTIONf_chiral_restr0.0661504
X-RAY DIFFRACTIONf_plane_restr0.0071932
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.747-1.76680.37231850.38913513X-RAY DIFFRACTION83
1.7668-1.78750.3962230.34794228X-RAY DIFFRACTION97
1.7875-1.80930.38752160.32864125X-RAY DIFFRACTION97
1.8093-1.83230.36752190.3064141X-RAY DIFFRACTION97
1.8323-1.85640.31572200.27174202X-RAY DIFFRACTION99
1.8564-1.88180.28912250.25554280X-RAY DIFFRACTION99
1.8818-1.90870.27552200.24664169X-RAY DIFFRACTION99
1.9087-1.93720.27062230.24384242X-RAY DIFFRACTION99
1.9372-1.96740.27342240.22654228X-RAY DIFFRACTION99
1.9674-1.99970.2422230.21584248X-RAY DIFFRACTION99
1.9997-2.03420.25522210.21174185X-RAY DIFFRACTION99
2.0342-2.07110.2742210.22044215X-RAY DIFFRACTION99
2.0711-2.1110.26382230.2064234X-RAY DIFFRACTION99
2.111-2.15410.23762210.20694192X-RAY DIFFRACTION98
2.1541-2.20090.30322160.20754095X-RAY DIFFRACTION96
2.2009-2.25210.25332240.19824245X-RAY DIFFRACTION99
2.2521-2.30840.22732240.20014255X-RAY DIFFRACTION99
2.3084-2.37080.2192230.19594251X-RAY DIFFRACTION99
2.3708-2.44060.2232230.18884254X-RAY DIFFRACTION99
2.4406-2.51930.23272240.19214242X-RAY DIFFRACTION99
2.5193-2.60930.21862230.19214231X-RAY DIFFRACTION99
2.6093-2.71380.22972240.184250X-RAY DIFFRACTION98
2.7138-2.83730.22842190.18814162X-RAY DIFFRACTION96
2.8373-2.98680.21532230.19534249X-RAY DIFFRACTION99
2.9868-3.17380.18992260.18624276X-RAY DIFFRACTION99
3.1738-3.41870.21022250.1714286X-RAY DIFFRACTION99
3.4187-3.76250.17542250.15874284X-RAY DIFFRACTION99
3.7625-4.30630.16112200.14114167X-RAY DIFFRACTION96
4.3063-5.42290.12922280.11794330X-RAY DIFFRACTION99
5.4229-37.7680.16922300.15724370X-RAY DIFFRACTION98
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)
14.84970.27432.00771.53890.43063.4337-0.03350.578-0.6007-0.1330.21270.16760.1259-0.0237-0.00910.2881-0.06730.03880.459-0.01520.305357.2426.11845.451
28.1423-1.08762.47782.8991-1.4633.6469-0.3033-0.3774-0.9557-0.11750.27960.2747-0.0127-0.34080.01930.3122-0.02630.06220.3886-0.01290.283759.7224.76453.506
35.5598-2.34334.6984.0778-3.12285.83550.0526-0.0491-0.7002-0.52610.30580.49250.4569-0.6206-0.27630.3384-0.030.05820.528-0.01760.335252.7997.60951.03
41.73060.01990.31291.1236-0.13261.8556-0.1356-0.0053-0.0568-0.07860.10240.0998-0.1084-0.16090.00670.2490.00130.03340.3744-0.00880.226461.95514.01648.52
51.54440.008-0.15061.1001-0.31526.8953-0.04110.10720.1971-0.15570.11150.168-0.47130.0723-0.07420.38430.0457-0.01740.4668-0.00740.292260.83724.85147.971
61.71060.2444-0.04612.11330.82152.3699-0.0890.17870.1561-0.27940.11620.0848-0.4513-0.0130.00910.28810.0227-0.00190.36240.02430.233862.25221.79744.032
72.1234-0.0244-0.48094.3767-3.91186.3662-0.0214-0.053-0.12750.20110.06620.2805-0.2827-0.4181-0.07190.25090.00790.02730.4411-0.01690.268654.02214.98656.672
82.9730.38850.47373.6782-2.75885.1602-0.2925-0.03110.2310.05640.33190.5478-0.3188-0.8976-0.1060.30950.0873-0.00550.5007-0.00940.34950.09719.80548.731
92.6044-0.05440.36762.7946-0.43625.6578-0.01920.3062-0.4113-0.3255-0.04430.04190.82120.3034-0.01570.3409-0.069-0.00590.3342-0.03420.339727.599-2.04270.101
101.97850.3905-0.17841.2186-0.01572.0888-0.04570.1672-0.146-0.19410.04330.09550.2022-0.0889-0.00350.2847-0.05240.00210.3521-0.02560.312430.4075.11771.577
111.8912-0.00430.5710.84320.08981.1641-0.10350.08190.0926-0.10360.02360.22990.0656-0.28790.07650.2397-0.04710.00960.37820.00210.327225.02913.58880.279
123.2159-0.7856-0.7461.19980.11731.8044-0.15850.1489-0.0708-0.10870.03790.13490.097-0.07130.12360.2469-0.06310.0190.3499-0.03490.321932.61414.32676.152
133.68393.1556-0.38484.1551-0.17482.0522-0.26420.51490.3651-0.72170.21570.62740.1043-0.3219-0.04570.293-0.046-0.09050.49750.02690.427921.73910.95868.267
142.416-0.83721.18761.6751-0.92093.8803-0.14180.05630.3821-0.1126-0.0282-0.0925-0.5558-0.19940.18680.40680.0117-0.08130.31240.00060.428530.40845.47180.899
152.8839-0.4687-1.01734.21580.51873.469-0.21870.30460.1672-0.4444-0.06910.4727-0.428-0.76920.31290.36740.0656-0.10290.5753-0.03640.454213.23937.50173.743
162.8249-0.41790.55341.631-0.61183.0712-0.3316-0.1840.2883-0.09220.17560.186-0.4541-0.23160.16850.32770.0362-0.07040.3366-0.04450.378626.62139.55486.932
171.238-0.4622-0.19731.07040.11271.8228-0.06250.1053-0.0421-0.1579-0.0688-0.0477-0.0198-0.05960.13340.2706-0.01410.00810.36880.01120.314333.33829.74682.613
183.1328-0.3332-0.2531.80970.6922.8304-0.1664-0.23450.0353-0.0589-0.00440.1797-0.1651-0.44830.17830.26860.0198-0.00990.3293-0.01550.325524.02430.67181.893
194.46512.23951.13484.07530.46692.5408-0.25430.34290.1454-0.5651-0.0086-0.2535-0.47250.01610.19540.3744-0.01560.01920.33570.03990.372732.50438.03973.26
204.7898-0.41692.28262.1085-0.54494.0156-0.309-0.34660.32980.33720.0934-0.0742-0.59450.53470.28610.39930.0932-0.0370.6788-0.16480.407834.5939.855114.374
213.4233-0.26170.53891.84920.65453.1212-0.1815-0.63840.21240.26960.03940.0292-0.0524-0.09490.1140.32410.10770.00840.6761-0.14870.380728.22836.116113.212
221.65460.12540.46711.98190.08912.2707-0.2662-0.59330.18390.2970.1492-0.3028-0.07010.46080.15110.26870.1233-0.03430.6754-0.0860.30741.00628.836109.641
233.50471.2911.92182.58271.27855.1654-0.1957-0.54950.18150.12930.1763-0.1399-0.45980.2580.12290.30740.0451-0.0420.6132-0.13330.37635.56839.161108.023
241.76140.13360.38551.46760.34691.7869-0.1928-0.3274-0.13910.1556-0.00790.17860.2181-0.29580.15520.27780.04240.06380.5565-0.00720.310427.03224.512104.174
252.50322.4795-0.74682.5776-0.46770.6959-0.2762-0.0073-0.29140.00990.1189-0.15110.2783-0.07430.10710.30380.0740.04110.5926-0.02910.28833.07622.178105.125
262.64990.76790.09892.1458-0.21282.6529-0.1166-0.30390.19860.16230.0419-0.03350.2530.05880.0590.30470.08320.02420.5635-0.05520.337438.27625.219105.889
275.0395-1.935-0.44241.91.11371.6623-0.4204-0.9951-0.15170.72590.23350.07590.4693-0.20070.11240.44080.13130.06090.7729-0.0030.340329.15226.54116.616
281.64940.1891-1.26742.7419-1.12224.365-0.0435-0.4814-0.5940.48640.13090.08130.8857-0.23530.05180.6276-0.0812-0.01930.57150.16970.490735.515-9.872101.043
291.899-0.5557-0.95112.4517-1.60522.2710.0873-0.2138-0.4510.250.2121-0.28450.73490.2182-0.20540.5946-0.0824-0.12060.37710.07790.459740.828-8.97996.974
301.9751-0.0794-0.16422.05440.41261.89530.0128-0.4732-0.290.57560.13110.20960.584-0.2869-0.09260.4853-0.07870.01110.46480.13510.307733.978-2.817101.674
311.5427-0.02030.66911.55040.51451.7923-0.0751-0.33520.0210.29390.1781-0.04240.3409-0.0193-0.11110.31170.00220.00780.41750.03640.311739.6169.12397.549
322.57722.5043-1.81423.067-1.19371.8050.0391-0.07180.56470.28930.05940.27710.3529-0.2822-0.08880.3224-0.03170.02480.54030.03230.278434.79710.606101.768
332.70490.857-0.19762.29760.15111.8436-0.073-0.3962-0.04370.40730.14920.22750.5492-0.3418-0.08810.3871-0.05770.05960.50710.08640.287430.266.734102.594
346.5147-2.6873-1.69853.27791.41152.6363-0.0842-0.562-0.18620.75670.2343-0.20540.63250.0713-0.31910.60330.0105-0.10320.53530.04650.358142.7311.124106.836
350.4158-0.1957-0.36661.69930.43831.9613-0.14350.29930.8752-0.21480.20050.2072-0.5138-0.5097-0.13360.87070.1469-0.25770.43260.15410.858959.74953.86143.923
362.1724-0.1553-0.17014.4828-0.35032.5572-0.1398-0.15960.63240.69630.480.4508-0.2519-0.4347-0.23360.69490.3086-0.04140.7073-0.00580.720148.2245.38459.108
372.1551-0.4731-0.13021.4402-0.13040.6973-0.250.29220.7823-0.04170.0840.1301-0.6022-0.28430.03680.75860.0837-0.19940.39630.03640.617666.91848.17847.107
381.50310.4486-0.6491.1342-0.42355.549-0.0720.07070.5277-0.04630.30620.2587-0.4947-0.4545-0.0410.62820.1099-0.13510.43570.02170.445159.66437.25649.37
392.2594-0.9285-2.46381.57431.76663.1224-0.17160.18420.4607-0.08690.21680.0407-0.05360.2814-0.0850.70010.0249-0.12270.49380.05970.419462.50737.27348.167
402.89760.507-0.35981.69250.87051.81-0.12670.09470.56430.00540.07020.1659-0.3285-0.55380.00910.56390.1432-0.10190.3996-0.00260.414760.77740.00652.746
410.3236-0.1024-0.94292.1939-1.59294.1556-0.3150.69050.8221-0.3075-0.1960.5826-0.4457-0.7935-0.60940.68990.1855-0.3930.6810.41990.608454.40444.33641.225
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:20 )A3 - 20
2X-RAY DIFFRACTION2( CHAIN A AND RESID 21:32 )A21 - 32
3X-RAY DIFFRACTION3( CHAIN A AND RESID 33:46 )A33 - 46
4X-RAY DIFFRACTION4( CHAIN A AND RESID 47:135 )A47 - 135
5X-RAY DIFFRACTION5( CHAIN A AND RESID 136:163 )A136 - 163
6X-RAY DIFFRACTION6( CHAIN A AND RESID 164:188 )A164 - 188
7X-RAY DIFFRACTION7( CHAIN A AND RESID 189:205 )A189 - 205
8X-RAY DIFFRACTION8( CHAIN A AND RESID 206:220 )A206 - 220
9X-RAY DIFFRACTION9( CHAIN B AND RESID 3:32 )B3 - 32
10X-RAY DIFFRACTION10( CHAIN B AND RESID 33:123 )B33 - 123
11X-RAY DIFFRACTION11( CHAIN B AND RESID 124:163 )B124 - 163
12X-RAY DIFFRACTION12( CHAIN B AND RESID 164:188 )B164 - 188
13X-RAY DIFFRACTION13( CHAIN B AND RESID 189:219 )B189 - 219
14X-RAY DIFFRACTION14( CHAIN C AND RESID 3:68 )C3 - 68
15X-RAY DIFFRACTION15( CHAIN C AND RESID 69:86 )C69 - 86
16X-RAY DIFFRACTION16( CHAIN C AND RESID 87:123 )C87 - 123
17X-RAY DIFFRACTION17( CHAIN C AND RESID 124:163 )C124 - 163
18X-RAY DIFFRACTION18( CHAIN C AND RESID 164:188 )C164 - 188
19X-RAY DIFFRACTION19( CHAIN C AND RESID 189:220 )C189 - 220
20X-RAY DIFFRACTION20( CHAIN D AND RESID 3:20 )D3 - 20
21X-RAY DIFFRACTION21( CHAIN D AND RESID 21:68 )D21 - 68
22X-RAY DIFFRACTION22( CHAIN D AND RESID 69:99 )D69 - 99
23X-RAY DIFFRACTION23( CHAIN D AND RESID 100:123 )D100 - 123
24X-RAY DIFFRACTION24( CHAIN D AND RESID 124:151 )D124 - 151
25X-RAY DIFFRACTION25( CHAIN D AND RESID 152:163 )D152 - 163
26X-RAY DIFFRACTION26( CHAIN D AND RESID 164:188 )D164 - 188
27X-RAY DIFFRACTION27( CHAIN D AND RESID 189:220 )D189 - 220
28X-RAY DIFFRACTION28( CHAIN E AND RESID 4:20 )E4 - 20
29X-RAY DIFFRACTION29( CHAIN E AND RESID 21:32 )E21 - 32
30X-RAY DIFFRACTION30( CHAIN E AND RESID 33:123 )E33 - 123
31X-RAY DIFFRACTION31( CHAIN E AND RESID 124:151 )E124 - 151
32X-RAY DIFFRACTION32( CHAIN E AND RESID 152:163 )E152 - 163
33X-RAY DIFFRACTION33( CHAIN E AND RESID 164:188 )E164 - 188
34X-RAY DIFFRACTION34( CHAIN E AND RESID 189:218 )E189 - 218
35X-RAY DIFFRACTION35( CHAIN F AND RESID 5:68 )F5 - 68
36X-RAY DIFFRACTION36( CHAIN F AND RESID 69:86 )F69 - 86
37X-RAY DIFFRACTION37( CHAIN F AND RESID 87:135 )F87 - 135
38X-RAY DIFFRACTION38( CHAIN F AND RESID 136:151 )F136 - 151
39X-RAY DIFFRACTION39( CHAIN F AND RESID 152:163 )F152 - 163
40X-RAY DIFFRACTION40( CHAIN F AND RESID 164:188 )F164 - 188
41X-RAY DIFFRACTION41( CHAIN F AND RESID 189:220 )F189 - 220

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