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- PDB-8b65: Structure of rsCherry crystallized in anaerobic conditions -

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Basic information

Entry
Database: PDB / ID: 8b65
TitleStructure of rsCherry crystallized in anaerobic conditions
ComponentsrsCherry
KeywordsFLUORESCENT PROTEIN / rsCherry / red fluorescent protein / chemical modifications
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 / molecular replacement / Resolution: 1.55 Å
AuthorsBui, T.Y.H. / Van Meervelt, L.
Funding supportViet Nam, Belgium, 2items
OrganizationGrant numberCountry
Other government911 projectViet Nam
KU Leuven Belgium
Citation
Journal: Int.J.Biol.Macromol. / Year: 2023
Title: Oxygen-induced chromophore degradation in the photoswitchable red fluorescent protein rsCherry.
Authors: Bui, T.Y.H. / De Zitter, E. / Moeyaert, B. / Pecqueur, L. / Srinivasu, B.Y. / Economou, A. / Fontecave, M. / Van Meervelt, L. / Dedecker, P. / Pedre, B.
#1: Journal: Biorxiv / Year: 2023
Title: Oxygen-induced chromophore degradation in the photoswitchable red fluorescent protein rsCherry
Authors: Bui, T.Y.H. / De Zitter, E. / Moeyaert, B. / Pecqueur, L. / Srinivasu, B.Y. / Economou, A. / Fontecave, M. / Van Meervelt, L. / Dedecker, P. / Pedre, B.
History
DepositionSep 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 19, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.ptnr1_label_atom_id
Revision 2.1Feb 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: rsCherry
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2276
Polymers30,7091
Non-polymers5185
Water4,846269
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint11 kcal/mol
Surface area10080 Å2
Unit cell
Length a, b, c (Å)61.170, 42.899, 108.566
Angle α, β, γ (deg.)90.000, 105.760, 90.000
Int Tables number5
Space group name H-MI121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein rsCherry


Mass: 30709.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Chromophore structures : QYX, Q2K / Source: (gene. exp.) Discosoma sp. (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9U6Y8

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Non-polymers , 5 types, 274 molecules

#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.56 Å3/Da / Density % sol: 51.93 %
Crystal growTemperature: 294.15 K / Method: microbatch / pH: 6 / Details: 18% PEG 8000 and 0.1M MES pH 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.55→46.2 Å / Num. obs: 39472 / % possible obs: 99.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 18.08 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.025 / Rrim(I) all: 0.065 / Net I/σ(I): 16.8 / Num. measured all: 267195 / Scaling rejects: 9
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
1.55-1.586.90.6871350119440.8490.2770.7422.699
8.49-46.25.90.0315532630.9990.0130.03346.598.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.82 Å46.2 Å
Translation2.82 Å46.2 Å

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Processing

Software
NameVersionClassification
XDS0.85data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H5Q

2h5q


Resolution: 1.55→46.2 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1786 1963 4.97 %
Rwork0.1512 37501 -
obs0.1525 39464 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.82 Å2 / Biso mean: 22.4133 Å2 / Biso min: 12.06 Å2
Refinement stepCycle: final / Resolution: 1.55→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1772 0 33 272 2077
Biso mean--39.2 34.33 -
Num. residues----221
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.590.24481510.20522644279598
1.59-1.630.22131460.191326202766100
1.63-1.680.20421460.18372629277599
1.68-1.730.21211520.17252653280599
1.73-1.80.20111430.163126682811100
1.8-1.870.20261400.16326492789100
1.87-1.950.19231400.149726932833100
1.95-2.060.1751230.143226632786100
2.06-2.180.17191390.145426922831100
2.18-2.350.21561470.158826782825100
2.35-2.590.19021310.160226832814100
2.59-2.960.18131330.153227092842100
2.97-3.730.15611430.138427202863100
3.74-46.20.14931290.139928002929100

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