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- PDB-9h25: Structure of rsCherry exposed to oxygen for 16 days -

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Basic information

Entry
Database: PDB / ID: 9h25
TitleStructure of rsCherry exposed to oxygen for 16 days
ComponentsrsCherry
KeywordsFLUORESCENT PROTEIN / rsCherry / red fluorescent protein / chemical modifications / chromophore 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: 1.9 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: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: rsCherry
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1594
Polymers29,9291
Non-polymers2303
Water3,855214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.391, 43.452, 108.818
Angle α, β, γ (deg.)90.00, 106.00, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein rsCherry / rsCherry


Mass: 29928.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: rsCherry / Source: (gene. exp.) Discosoma sp. (sea anemone) / Gene: PAmCherry, PAmCherry1 / 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.27 Å3/Da / Density % sol: 45.93 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 6 / Details: PEG 8000 16%, 0.1M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→46.23 Å / Num. obs: 21952 / % possible obs: 99.8 % / Redundancy: 6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.044 / Rrim(I) all: 0.109 / Χ2: 0.73 / Net I/σ(I): 10 / Num. measured all: 131845
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible allMean I/σ(I) obs
1.9-1.9450.26513630.9560.1290.2960.4598.8
9.11-46.235.50.0772220.9940.0360.0859916.2

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
Aimless0.7.4data scaling
DIALS2.1.3data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46.23 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1904 1158 5.28 %
Rwork0.1557 --
obs0.1576 21944 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→46.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1789 0 15 214 2018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018
X-RAY DIFFRACTIONf_angle_d1.672
X-RAY DIFFRACTIONf_dihedral_angle_d22.382713
X-RAY DIFFRACTIONf_chiral_restr0.241250
X-RAY DIFFRACTIONf_plane_restr0.019334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.990.25191310.17032560X-RAY DIFFRACTION99
1.99-2.090.19031480.15332577X-RAY DIFFRACTION100
2.09-2.220.20141510.14932562X-RAY DIFFRACTION100
2.22-2.390.21821380.16452585X-RAY DIFFRACTION100
2.39-2.630.19111470.15932588X-RAY DIFFRACTION100
2.63-3.020.19531510.15962608X-RAY DIFFRACTION100
3.02-3.80.16911330.14962635X-RAY DIFFRACTION100
3.8-46.230.17991590.15372671X-RAY DIFFRACTION100

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