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- PDB-9mus: Reduced state of a turn-off thiol-disulfide redox biosensor with ... -

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Basic information

Entry
Database: PDB / ID: 9mus
TitleReduced state of a turn-off thiol-disulfide redox biosensor with a fluorescence-lifetime readout
ComponentsFluorescent thiol-disulfide redox biosensor
KeywordsFLUORESCENT PROTEIN / fluorescence lifetime / thiol-disulfide redox
Function / homologyACETIC ACID / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRosen, P. / Yellen, G. / Lim, D.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM124038 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Mechanism and application of thiol-disulfide redox biosensors with a fluorescence-lifetime readout.
Authors: Rosen, P.C. / Glaser, A. / Martinez-Francois, J.R. / Lim, D.C. / Brooks, D.J. / Fu, P. / Kim, E. / Kern, D. / Yellen, G.
History
DepositionJan 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Database references / Refinement description / Structure summary
Category: pdbx_entry_details / refine ...pdbx_entry_details / refine / software / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _pdbx_entry_details.sequence_details / _refine.ls_number_reflns_R_free ..._pdbx_entry_details.sequence_details / _refine.ls_number_reflns_R_free / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fluorescent thiol-disulfide redox biosensor
B: Fluorescent thiol-disulfide redox biosensor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2557
Polymers56,8002
Non-polymers4545
Water5,080282
1
A: Fluorescent thiol-disulfide redox biosensor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4602
Polymers28,4001
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fluorescent thiol-disulfide redox biosensor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7945
Polymers28,4001
Non-polymers3944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.800, 140.180, 130.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-543-

HOH

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Components

#1: Protein Fluorescent thiol-disulfide redox biosensor


Mass: 28400.020 Da / Num. of mol.: 2
Mutation: Based on GFP, Y66W in the chromophore, numerous other mutations relative to GFP
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY
Sequence detailsChromophore SWG 66 formed from Ser-Trp-Gly in the translated sequence

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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: 2.12 Å3/Da / Density % sol: 41.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 2.5% glycerol, 5% Tacsimate (pH 4.0), 0.1 M sodium acetate (pH 5.2), 16% PEG 3350, 10 mM TCEP (pH ~7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30.85 Å / Num. obs: 32802 / % possible obs: 99.08 % / Redundancy: 9.1 % / CC1/2: 0.997 / Net I/σ(I): 11.28
Reflection shellResolution: 2→2.072 Å / Num. unique obs: 14547 / CC1/2: 0.664

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30.85 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2246 1999 -
Rwork0.1859 --
obs-32801 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→30.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3576 0 30 282 3888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023745
X-RAY DIFFRACTIONf_angle_d1.1715064
X-RAY DIFFRACTIONf_dihedral_angle_d11.2571381
X-RAY DIFFRACTIONf_chiral_restr0.045541
X-RAY DIFFRACTIONf_plane_restr0.003659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.28041230.29041914X-RAY DIFFRACTION87
2.03-2.050.29451250.29031987X-RAY DIFFRACTION93
2.05-2.080.29581400.27772149X-RAY DIFFRACTION96
2.08-2.110.31261400.26082118X-RAY DIFFRACTION97
2.11-2.140.32761420.26062198X-RAY DIFFRACTION99
2.14-2.170.28421430.2412179X-RAY DIFFRACTION100
2.17-2.210.2911390.23322188X-RAY DIFFRACTION100
2.21-2.250.31171390.21232169X-RAY DIFFRACTION100
2.25-2.290.29121470.2092185X-RAY DIFFRACTION100
2.29-2.330.2581390.20872230X-RAY DIFFRACTION100
2.33-2.380.24831350.1972172X-RAY DIFFRACTION100
2.38-2.430.25391410.20152202X-RAY DIFFRACTION100
2.43-2.490.2411400.19662181X-RAY DIFFRACTION100
2.49-2.550.21430.20162174X-RAY DIFFRACTION100
2.55-2.620.26281370.20582218X-RAY DIFFRACTION100
2.62-2.70.24851460.19422199X-RAY DIFFRACTION100
2.7-2.780.2451450.1922206X-RAY DIFFRACTION100
2.78-2.880.25321410.1972167X-RAY DIFFRACTION100
2.88-30.1981430.18622199X-RAY DIFFRACTION100
3-3.140.23171360.17742171X-RAY DIFFRACTION100
3.14-3.30.24371440.17262198X-RAY DIFFRACTION99
3.3-3.510.21551400.15962167X-RAY DIFFRACTION99
3.51-3.780.17351400.14772157X-RAY DIFFRACTION99
3.78-4.160.17221410.14322140X-RAY DIFFRACTION98
4.16-4.760.1651370.13172166X-RAY DIFFRACTION98
4.76-5.990.18261370.17012161X-RAY DIFFRACTION99
5.99-30.850.22511370.21852109X-RAY DIFFRACTION96
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)
14.2298-2.64193.4573.7512-2.02294.5491-0.2352-0.31520.3229-0.05550.0090.2905-0.3902-0.46360.24940.13720.03290.09710.21560.00070.16413.11212.33415.76
24.58541.40813.96452.56481.40694.7367-0.04240.06920.1823-0.0858-0.0163-0.2143-0.17860.03060.05430.1378-0.02080.05290.16470.01750.174313.20311.34514.605
35.6051-3.42391.19537.37072.65615.71260.19490.3434-0.38640.070.07050.36860.0553-0.3767-0.25720.1936-0.0405-0.01140.25150.05390.2241-5.004-0.9438.682
44.7816-0.6871.58721.37370.01711.8862-0.0219-0.1493-0.01220.1240.0714-0.0850.0419-0.0798-0.05780.199-0.03790.02680.14840.03090.17111.115.16720.979
56.5098-2.74080.82733.30420.62161.6673-0.1074-0.2079-0.10590.13610.173-0.03080.2861-0.15460.00220.278-0.0535-0.01570.18010.03770.18768.734-4.0820.457
61.57212.38870.65193.82770.6421.4232-0.09030.0796-0.0801-0.14020.1276-0.08830.0068-0.1325-0.05910.15050.0302-0.0120.20070.04620.22127.4355.06511.048
74.4247-1.3145-6.16343.39951.81098.3785-0.28350.1315-0.67-0.2902-0.044-0.12680.1333-0.06420.25020.20290.0012-0.06790.18550.02450.1205-0.073-36.8816.768
87.17391.3078-2.38293.42710.37062.99160.00410.2688-0.1346-0.30670.07870.144-0.0776-0.1388-0.08520.2519-0.0288-0.07470.15790.01850.1518-9.038-35.63314.461
93.01484.0651-1.44166.0005-2.09046.7205-0.44180.90220.0224-0.70440.3512-0.5677-0.55920.39470.07450.4508-0.13280.01740.35180.05930.32579.634-23.8669.637
108.2182-2.2277-2.41042.60861.00142.5289-0.1182-0.24580.10270.21610.0915-0.0532-0.11420.14610.03030.2332-0.0384-0.03910.15610.02680.1254-1.479-31.48322.547
114.25150.49183.01772.16471.90383.8522-0.23320.08940.0501-0.19040.12690.5612-0.1993-0.55940.0210.30380.0332-0.02210.18370.06580.4904-19.537-24.87717.795
125.7316-2.53671.1213.6792-1.3370.9883-0.20750.01870.00260.31820.05780.0609-0.34850.08810.15930.364-0.0488-0.01640.20870.00010.1549-1.048-21.00320.633
135.89336.2968-0.23877.7396-0.56921.2313-0.23440.26640.4449-0.6270.21970.4981-0.16460.0538-0.00210.3626-0.0335-0.05270.22650.0320.2485-8.053-31.1758.111
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:24 )A3 - 24
2X-RAY DIFFRACTION2( CHAIN A AND RESID 25:68 )A25 - 68
3X-RAY DIFFRACTION3( CHAIN A AND RESID 69:81 )A69 - 81
4X-RAY DIFFRACTION4( CHAIN A AND RESID 82:150 )A82 - 150
5X-RAY DIFFRACTION5( CHAIN A AND RESID 151:188 )A151 - 188
6X-RAY DIFFRACTION6( CHAIN A AND RESID 189:230 )A189 - 230
7X-RAY DIFFRACTION7( CHAIN B AND RESID 3:24 )B3 - 24
8X-RAY DIFFRACTION8( CHAIN B AND RESID 25:68 )B25 - 68
9X-RAY DIFFRACTION9( CHAIN B AND RESID 69:81 )B69 - 81
10X-RAY DIFFRACTION10( CHAIN B AND RESID 82:128 )B82 - 128
11X-RAY DIFFRACTION11( CHAIN B AND RESID 129:150 )B129 - 150
12X-RAY DIFFRACTION12( CHAIN B AND RESID 151:199 )B151 - 199
13X-RAY DIFFRACTION13( CHAIN B AND RESID 200:230 )B200 - 230

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