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- PDB-3u8c: Crystal structure of monomeric reversibly photoswitchable red flu... -

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Basic information

Entry
Database: PDB / ID: 3u8c
TitleCrystal structure of monomeric reversibly photoswitchable red fluorescent protein rsTagRFP in the ON state
ComponentsFluorescent protein rsTagRFP
KeywordsFLUORESCENT PROTEIN / beta barrel / light induced reversible photoswitching / reversibly photoswitchable fluorescent protein / cis-trans isomerization
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.188 Å
AuthorsPletnev, S.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: A structural basis for reversible photoswitching of absorbance spectra in red fluorescent protein rsTagRFP.
Authors: Pletnev, S. / Subach, F.V. / Dauter, Z. / Wlodawer, A. / Verkhusha, V.V.
History
DepositionOct 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Database references
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fluorescent protein rsTagRFP
B: Fluorescent protein rsTagRFP
C: Fluorescent protein rsTagRFP
D: Fluorescent protein rsTagRFP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,6505
Polymers110,5584
Non-polymers921
Water9,476526
1
A: Fluorescent protein rsTagRFP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7322
Polymers27,6391
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fluorescent protein rsTagRFP


Theoretical massNumber of molelcules
Total (without water)27,6391
Polymers27,6391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fluorescent protein rsTagRFP


Theoretical massNumber of molelcules
Total (without water)27,6391
Polymers27,6391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Fluorescent protein rsTagRFP


Theoretical massNumber of molelcules
Total (without water)27,6391
Polymers27,6391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.564, 69.336, 73.699
Angle α, β, γ (deg.)78.690, 83.600, 71.970
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Fluorescent protein rsTagRFP


Mass: 27639.455 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 blue
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M Ammonium Citrate, 20% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.188→30 Å / Num. obs: 45928 / % possible obs: 98.1 % / Redundancy: 2 % / Rmerge(I) obs: 0.048 / Χ2: 0.906 / Net I/σ(I): 9.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.188-2.281.90.33845400.83196.8
2.28-2.3720.25645770.88197.3
2.37-2.4820.19645920.865197.7
2.48-2.6120.14645560.849197.7
2.61-2.7720.10546090.911198.1
2.77-2.9920.07645460.97198.2
2.99-3.2920.05146261.015198.4
3.29-3.7620.0446400.941198.7
3.76-4.7320.03445990.842198.9
4.73-3020.02746430.951198.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.188→26.887 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.8114 / SU ML: 0.32 / σ(F): 1.97 / Phase error: 26.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2441 1434 3.12 %
Rwork0.1603 44479 -
obs0.1628 45913 97.27 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.062 Å2 / ksol: 0.379 e/Å3
Displacement parametersBiso max: 155.94 Å2 / Biso mean: 46.9473 Å2 / Biso min: 12.44 Å2
Baniso -1Baniso -2Baniso -3
1-5.274 Å2-8.2462 Å21.3396 Å2
2--1.551 Å20.8329 Å2
3----6.825 Å2
Refinement stepCycle: LAST / Resolution: 2.188→26.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7144 0 6 526 7676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0197429
X-RAY DIFFRACTIONf_angle_d1.95710049
X-RAY DIFFRACTIONf_chiral_restr0.1151040
X-RAY DIFFRACTIONf_plane_restr0.0091300
X-RAY DIFFRACTIONf_dihedral_angle_d15.4362790
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.188-2.26560.37761270.24874112423989
2.2656-2.35630.28261460.20514466461297
2.3563-2.46350.29631400.18744469460998
2.4635-2.59330.27991550.18624446460198
2.5933-2.75560.27631620.1734471463398
2.7556-2.96810.27081220.16864444456698
2.9681-3.26630.28061480.15734538468698
3.2663-3.73790.21631360.1564495463199
3.7379-4.70520.20341540.13124512466699
4.7052-26.88930.21981440.15154526467099
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)
10.84350.02140.30781.6484-0.29681.97190.1599-0.0216-0.0377-0.262-0.13660.06810.4283-0.207700.20430.0325-0.02210.165-0.01610.1456-0.21110.6604-0.0347
20.60790.6779-0.01983.1104-0.42991.38750.2251-0.2795-0.17060.2036-0.268-0.22230.3142-0.0986-00.23180.0072-0.04390.22180.03460.24794.5461-6.891830.7241
30.85790.3985-0.23941.6275-0.22411.48260.3009-0.33320.08340.2584-0.2923-0.0149-0.42820.22580.00020.2444-0.08680.02330.2708-0.0340.17218.7222.373136.6462
41.40890.90470.0672.24370.0841.91650.06620.06730.1372-0.3355-0.0783-0.2067-0.60750.2556-00.2862-0.03740.04150.18390.02420.213713.541126.98275.3639
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA3 - 228
2X-RAY DIFFRACTION2chain BB3 - 228
3X-RAY DIFFRACTION3chain CC3 - 228
4X-RAY DIFFRACTION4chain DD3 - 228

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