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- PDB-9jx2: Structure of rsCherry exposed to oxygen for 8 days -

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Basic information

Entry
Database: PDB / ID: 9jx2
TitleStructure of rsCherry exposed to oxygen for 8 days
ComponentsRed fluorescent protein drFP583
KeywordsFLUORESCENT PROTEIN / red fluorescent protein / reversibly switching / degradation
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / DI(HYDROXYETHYL)ETHER / Red fluorescent protein drFP583
Function and homology information
Biological speciesDiscosoma sp. (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBui, T.Y.H. / Van Meervelt, L.
Funding support Belgium, 1items
OrganizationGrant numberCountry
KU Leuven Belgium
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Crystal structure analysis of oxygen-induced degradation occurring in rsCherry.
Authors: Bui, T.Y.H. / Pecqueur, L. / Dedecker, P. / Van Meervelt, L.
History
DepositionOct 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Red fluorescent protein drFP583
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3112
Polymers31,2051
Non-polymers1061
Water2,756153
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)61.189, 42.765, 108.226
Angle α, β, γ (deg.)90.00, 105.90, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Red fluorescent protein drFP583 / DsRed


Mass: 31204.947 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Chromophores: Q2K, QIP, QYX / Source: (gene. exp.) Discosoma sp. (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9U6Y8
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 6 / Details: 16% PEG 8000 , 0.1 M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2→39.56 Å / Num. obs: 18465 / % possible obs: 100 % / Redundancy: 5.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.046 / Rrim(I) all: 0.109 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.055.60.6722.313640.8250.3130.743100
8.94-39.560.03534.22310.9980.0160.03898.8

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
Aimless0.7.4data scaling
XDSdata reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8B65

8b65


Resolution: 2→39.56 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2172 872 4.73 %
Rwork0.1752 --
obs0.1772 18445 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→39.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1766 0 7 153 1926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d0.939
X-RAY DIFFRACTIONf_dihedral_angle_d20.698706
X-RAY DIFFRACTIONf_chiral_restr0.21248
X-RAY DIFFRACTIONf_plane_restr0.004330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.130.28821340.23562932X-RAY DIFFRACTION100
2.13-2.290.24171340.2092888X-RAY DIFFRACTION100
2.29-2.520.26131470.19722910X-RAY DIFFRACTION100
2.52-2.880.24451550.18572917X-RAY DIFFRACTION100
2.88-3.630.24131560.16642936X-RAY DIFFRACTION100
3.63-39.560.1631460.15092990X-RAY DIFFRACTION100

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