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- PDB-8c0n: Crystal structure of the red form of the mTagFT fluorescent timer -

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Basic information

Entry
Database: PDB / ID: 8c0n
TitleCrystal structure of the red form of the mTagFT fluorescent timer
ComponentsBlue-to-red TagFT fluorescent timer
KeywordsFLUORESCENT PROTEIN / timer / blue-to-red / TagFT / genetically encoded / red form / LYG
Function / homologyGreen fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Red fluorescent protein eqFP611
Function and homology information
Biological speciesEntacmaea quadricolor (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBoyko, K.M. / Nikolaeva, A.Y. / Vlaskina, A.V. / Agapova, Y.K. / Subach, O.M. / Popov, V.O. / Subach, F.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation21-74-20135 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2023
Title: Blue-to-Red TagFT, mTagFT, mTsFT, and Green-to-FarRed mNeptusFT2 Proteins, Genetically Encoded True and Tandem Fluorescent Timers.
Authors: Subach, O.M. / Vlaskina, A.V. / Agapova, Y.K. / Nikolaeva, A.Y. / Anokhin, K.V. / Piatkevich, K.D. / Patrushev, M.V. / Boyko, K.M. / Subach, F.V.
History
DepositionDec 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / entity_name_com / entity_src_gen / pdbx_validate_main_chain_plane / pdbx_validate_torsion / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
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 / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _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_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Blue-to-red TagFT fluorescent timer
B: Blue-to-red TagFT fluorescent timer
C: Blue-to-red TagFT fluorescent timer
D: Blue-to-red TagFT fluorescent timer


Theoretical massNumber of molelcules
Total (without water)124,9264
Polymers124,9264
Non-polymers00
Water72140
1
A: Blue-to-red TagFT fluorescent timer


Theoretical massNumber of molelcules
Total (without water)31,2311
Polymers31,2311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Blue-to-red TagFT fluorescent timer


Theoretical massNumber of molelcules
Total (without water)31,2311
Polymers31,2311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Blue-to-red TagFT fluorescent timer


Theoretical massNumber of molelcules
Total (without water)31,2311
Polymers31,2311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Blue-to-red TagFT fluorescent timer


Theoretical massNumber of molelcules
Total (without water)31,2311
Polymers31,2311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.645, 95.317, 95.383
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein
Blue-to-red TagFT fluorescent timer / GFP-like chromoprotein


Mass: 31231.402 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entacmaea quadricolor (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ISF8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.21 Å3/Da / Density % sol: 44.26 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0,2 M Lithium sulfate, 0.1M Bis-tris pH 6.5, 27% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.9→95.38 Å / Num. obs: 23481 / % possible obs: 97.3 % / Redundancy: 2.6 % / CC1/2: 0.974 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.123 / Rrim(I) all: 0.206 / Χ2: 0.91 / Net I/σ(I): 4.7 / Num. measured all: 61067
Reflection shellResolution: 2.9→3.08 Å / % possible obs: 98.2 % / Redundancy: 2.5 % / Rmerge(I) obs: 1.191 / Num. measured all: 9558 / Num. unique obs: 3823 / CC1/2: 0.337 / Rpim(I) all: 0.945 / Rrim(I) all: 1.528 / Χ2: 0.81 / Net I/σ(I) obs: 1.1

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Processing

Software
NameClassification
BUSTERrefinement
Aimlessdata scaling
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M22

3m22


Resolution: 2.9→95.32 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.904 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.421
RfactorNum. reflection% reflectionSelection details
Rfree0.2773 1023 4.37 %RANDOM
Rwork0.2423 ---
obs0.2438 23426 96.8 %-
Displacement parametersBiso mean: 73.27 Å2
Baniso -1Baniso -2Baniso -3
1-4.6786 Å20 Å22.5345 Å2
2---1.473 Å20 Å2
3----3.2056 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: LAST / Resolution: 2.9→95.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6703 0 64 40 6807
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086944HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.089430HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2318SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1184HARMONIC5
X-RAY DIFFRACTIONt_it6944HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion19.32
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion903SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5125SEMIHARMONIC4
LS refinement shellResolution: 2.9→2.92 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.4778 -5.33 %
Rwork0.3423 444 -
all0.3488 469 -
obs--96.62 %
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)
14.23831.50581.16944.41430.56084.28810.0034-0.2144-0.0078-0.0869-0.11190.014-0.2225-0.34520.1085-0.291-0.00510.01440.0864-0.0901-0.2021-14.3244-38.576863.6976
23.9941-1.25541.40253.4368-0.03884.5479-0.00770.0159-0.28030.15130.11860.3348-0.023-0.0629-0.1109-0.21950.01180.0187-0.11380.10050.0741-14.326-16.41779.3312
34.28371.0477-1.41674.0999-0.34254.39420.00740.06230.2599-0.24990.11540.33960.1072-0.0393-0.1228-0.2941-0.02150.0392-0.15460.11180.016-14.371415.8097-9.4104
43.5844-1.1322-1.1494.6240.48654.1483-0.03940.2198-0.02930.1106-0.07640.09580.187-0.37690.1158-0.3430.01650.02840.0349-0.0961-0.2671-14.3051-57.165631.5995
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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