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- PDB-9h27: Structure of rsCherry exposed to oxygen for 90 days -

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Basic information

Entry
Database: PDB / ID: 9h27
TitleStructure of rsCherry exposed to oxygen for 90 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: 1.7 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)30,2314
Polymers29,8371
Non-polymers3933
Water3,963220
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.227, 43.164, 108.112
Angle α, β, γ (deg.)90.00, 106.08, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein rsCherry / rsCherry


Mass: 29837.385 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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 294 K / Method: microbatch / Details: PEG 8000 17%, 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 XE 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: 1.7→39.86 Å / Num. obs: 30118 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.027 / Rrim(I) all: 0.069 / Χ2: 0.79 / Net I/σ(I): 14.9 / Num. measured all: 194796
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2Mean I/σ(I) obs% possible all
1.7-1.736.60.56415980.9060.2350.6120.52
9-39.866.20.0392260.9990.0160.04235.198.7

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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: 1.7→39.86 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1887 1495 4.97 %
Rwork0.1558 --
obs0.1574 30105 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→39.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1766 0 19 220 2005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d1.106
X-RAY DIFFRACTIONf_dihedral_angle_d21.325732
X-RAY DIFFRACTIONf_chiral_restr0.213253
X-RAY DIFFRACTIONf_plane_restr0.009334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.25621470.20792581X-RAY DIFFRACTION100
1.75-1.820.19681480.1772537X-RAY DIFFRACTION100
1.82-1.890.23581340.17882587X-RAY DIFFRACTION100
1.89-1.980.18781620.15922574X-RAY DIFFRACTION100
1.98-2.080.18291270.14652601X-RAY DIFFRACTION100
2.08-2.210.19491250.14972576X-RAY DIFFRACTION100
2.21-2.380.20681310.16052588X-RAY DIFFRACTION100
2.38-2.620.17361310.16082601X-RAY DIFFRACTION100
2.62-30.20061260.1572633X-RAY DIFFRACTION100
3-3.780.17551380.14252628X-RAY DIFFRACTION100
3.78-39.860.17511260.15322704X-RAY DIFFRACTION100

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