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- PDB-7qgk: The mRubyFT protein, Genetically Encoded Blue-to-Red Fluorescent ... -

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Basic information

Entry
Database: PDB / ID: 7qgk
TitleThe mRubyFT protein, Genetically Encoded Blue-to-Red Fluorescent Timer in its red state
ComponentsThe red form of the mRubyFT protein, Genetically Encoded Blue-to-Red Fluorescent Timer
KeywordsFLUORESCENT PROTEIN / flourescent timer / mRubyFT / blue to red timer / chromophore
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 / molecular replacement / Resolution: 1.5 Å
AuthorsBoyko, K.M. / Nikolaeva, A.Y. / Gaivoronskii, F.A. / Vlaskina, A.V. / 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: 2022
Title: The mRubyFT Protein, Genetically Encoded Blue-to-Red Fluorescent Timer.
Authors: Subach, O.M. / Tashkeev, A. / Vlaskina, A.V. / Petrenko, D.E. / Gaivoronskii, F.A. / Nikolaeva, A.Y. / Ivashkina, O.I. / Anokhin, K.V. / Popov, V.O. / Boyko, K.M. / Subach, F.V.
History
DepositionDec 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Apr 12, 2023Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity_name_com / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_mod_residue / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_poly_seq_scheme.pdb_seq_num / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_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
Revision 3.0Nov 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 / 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 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 3.1Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: The red form of the mRubyFT protein, Genetically Encoded Blue-to-Red Fluorescent Timer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0894
Polymers27,0161
Non-polymers733
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.338, 66.253, 96.496
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein The red form of the mRubyFT protein, Genetically Encoded Blue-to-Red Fluorescent Timer / GFP-like chromoprotein


Mass: 27015.939 Da / Num. of mol.: 1
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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 1.85 Å3/Da / Density % sol: 33.66 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / Details: 0.1M bis-tris pH 5.5; 21% 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: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→96.5 Å / Num. obs: 33034 / % possible obs: 99.8 % / Redundancy: 7.9 % / CC1/2: 1 / Rmerge(I) obs: 0.025 / Rpim(I) all: 0.01 / Rrim(I) all: 0.027 / Net I/σ(I): 40.2 / Num. measured all: 259961
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.537.20.2091147815900.9730.0830.2254.3100
8.22-96.56.20.02115042420.9960.010.023116.895.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
Aimless0.7.7data scaling
MOLREPphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U0L

3u0l


Resolution: 1.5→54.62 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.443 / SU ML: 0.046 / SU R Cruickshank DPI: 0.0774 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1949 1616 4.9 %RANDOM
Rwork0.1738 ---
obs0.1748 31353 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.32 Å2 / Biso mean: 20.087 Å2 / Biso min: 12 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å20 Å2
2---0.18 Å20 Å2
3---0.12 Å2
Refinement stepCycle: final / Resolution: 1.5→54.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 488 156 2362
Biso mean--21.83 30.22 -
Num. residues----158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131881
X-RAY DIFFRACTIONr_bond_other_d0.0060.0151754
X-RAY DIFFRACTIONr_angle_refined_deg2.0591.6762541
X-RAY DIFFRACTIONr_angle_other_deg1.5191.5934069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0835227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61921.553103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99715339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4481514
X-RAY DIFFRACTIONr_chiral_restr0.1140.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022094
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02439
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 132 -
Rwork0.195 2257 -
all-2389 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -1.7809 Å / Origin y: 8.4422 Å / Origin z: -21.8181 Å
111213212223313233
T0.0095 Å20.0028 Å20.0021 Å2-0.0069 Å20.0027 Å2--0.0038 Å2
L0.6005 °2-0.0037 °2-0.1383 °2-0.4541 °20.2805 °2--1.0947 °2
S-0.0363 Å °0.0297 Å °-0.012 Å °-0.0533 Å °-0.0237 Å °0.0045 Å °0.0045 Å °0.0386 Å °0.0599 Å °

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