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- PDB-7sf9: Branchiostoma Floridae Violet Fluorescent Protein -

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Basic information

Entry
Database: PDB / ID: 7sf9
TitleBranchiostoma Floridae Violet Fluorescent Protein
ComponentsViolet Fluorescent Protein
KeywordsFLUORESCENT PROTEIN / oxidized tyrosine / chromophore
Biological speciesBranchiostoma floridae (Florida lancelet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPletnev, S. / Pletneva, N. / Pletnev, V.Z. / Muslinkina, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Protein Sci. / Year: 2022
Title: A novel violet fluorescent protein contains a unique oxidized tyrosine as the simplest chromophore ever reported in fluorescent proteins.
Authors: Roldan-Salgado, A. / Muslinkina, L. / Pletnev, S. / Pletneva, N. / Pletnev, V. / Gaytan, P.
History
DepositionOct 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Violet Fluorescent Protein
B: Violet Fluorescent Protein
C: Violet Fluorescent Protein
D: Violet Fluorescent Protein


Theoretical massNumber of molelcules
Total (without water)107,6974
Polymers107,6974
Non-polymers00
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-31 kcal/mol
Surface area34540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.674, 177.674, 52.362
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
Violet Fluorescent Protein


Mass: 26924.309 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Branchiostoma floridae (Florida lancelet)
Gene: BRAFLDRAFT_75522 / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.22 Å3/Da / Density % sol: 44.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1.35 M Li2SO4, 0.09 M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→153.87 Å / Num. obs: 87717 / % possible obs: 99.9 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 38.05
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.822 / Num. unique obs: 8647 / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0103refinement
PDB_EXTRACT3.27data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M9X

6m9x


Resolution: 1.8→153.87 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.897 / SU ML: 0.116 / SU R Cruickshank DPI: 0.1467 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2632 1647 2 %RANDOM
Rwork0.2091 ---
obs0.2102 82352 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.09 Å2 / Biso mean: 26.914 Å2 / Biso min: 5.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.06 Å20 Å2
2--0.11 Å2-0 Å2
3----0.37 Å2
Refinement stepCycle: final / Resolution: 1.8→153.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7031 0 0 403 7434
Biso mean---25.69 -
Num. residues----883
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0197392
X-RAY DIFFRACTIONr_bond_other_d0.0030.026778
X-RAY DIFFRACTIONr_angle_refined_deg2.1251.95210015
X-RAY DIFFRACTIONr_angle_other_deg1.27315713
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1755904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.72624.311334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.367151240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8751523
X-RAY DIFFRACTIONr_chiral_restr0.1280.21029
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0218451
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021780
LS refinement shellResolution: 1.801→1.848 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 63 -
Rwork0.304 3434 -
all-3497 -
obs--54.35 %

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