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- PDB-9irj: X-ray structure of PSmOrange3 (trigonal form) -

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Basic information

Entry
Database: PDB / ID: 9irj
TitleX-ray structure of PSmOrange3 (trigonal form)
ComponentsmOrange
KeywordsFLUORESCENT PROTEIN / CHROMOPHORE / photoswitching
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / metal ion binding / mOrange
Function and homology information
Biological speciesDiscosoma sp. (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSamygina, V.R. / Subach, O.M. / Vlaskina, A.V. / Nikolaeva, A.Y. / Subach, F.V.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: Genetically Encoded Orange-to-Far-red Photoconvertible Fluorescent Protein PSmOrange3
Authors: Subach, O.M. / Samygina, V.R. / Vlaskina, A.V. / Nikolaeva, A.Y. / Subach, F.V.
History
DepositionJul 16, 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

Downloads & links

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Assembly

Deposited unit
A: mOrange


Theoretical massNumber of molelcules
Total (without water)26,5581
Polymers26,5581
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.165, 137.165, 55.223
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein mOrange


Mass: 26558.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CRO IS PEPTIDE DERIVED CHROMOPHORE 71TYG73 / Source: (gene. exp.) Discosoma sp. (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: D0VWW2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 5.61 Å3/Da / Density % sol: 78.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: Na/K Phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.8→68.59 Å / Num. obs: 15169 / % possible obs: 100 % / Redundancy: 19.1 % / CC1/2: 0.98 / Net I/σ(I): 6.3
Reflection shellResolution: 2.8→2.94 Å / Num. unique obs: 608 / CC1/2: 0.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→68.59 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.211 / WRfactor Rwork: 0.18 / SU B: 8.972 / SU ML: 0.161 / Average fsc free: 0.9139 / Average fsc work: 0.9233 / Cross valid method: FREE R-VALUE / ESU R: 0.274 / ESU R Free: 0.222
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2099 651 5.04 %
Rwork0.1783 13303 -
all0.18 --
obs-14009 93.599 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 55.401 Å2
Baniso -1Baniso -2Baniso -3
1--0.164 Å2-0.082 Å2-0 Å2
2---0.164 Å20 Å2
3---0.533 Å2
Refinement stepCycle: LAST / Resolution: 2.8→68.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1715 0 22 18 1755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131783
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171645
X-RAY DIFFRACTIONr_angle_refined_deg2.1931.6722397
X-RAY DIFFRACTIONr_angle_other_deg1.3471.5983833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.325213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68422.75987
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.46915317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.965158
X-RAY DIFFRACTIONr_chiral_restr0.0740.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021959
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02377
X-RAY DIFFRACTIONr_nbd_refined0.2080.2314
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.21557
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2834
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1050.2973
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.238
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.010.22
X-RAY DIFFRACTIONr_nbd_other0.1810.217
X-RAY DIFFRACTIONr_mcbond_it4.5515.245858
X-RAY DIFFRACTIONr_mcbond_other4.4855.237857
X-RAY DIFFRACTIONr_mcangle_it6.6257.8571069
X-RAY DIFFRACTIONr_mcangle_other6.6247.8681070
X-RAY DIFFRACTIONr_scbond_it7.5996.292925
X-RAY DIFFRACTIONr_scbond_other7.5966.297926
X-RAY DIFFRACTIONr_scangle_it11.6779.0311328
X-RAY DIFFRACTIONr_scangle_other11.6739.0371329
X-RAY DIFFRACTIONr_lrange_it14.91161.7221892
X-RAY DIFFRACTIONr_lrange_other14.91761.7861893
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.8730.354330.295608X-RAY DIFFRACTION59.2421
2.873-2.9510.321340.307732X-RAY DIFFRACTION72.3324
2.951-3.0370.335360.292869X-RAY DIFFRACTION86.7689
3.037-3.130.257390.251894X-RAY DIFFRACTION93.3934
3.13-3.2320.338550.255913X-RAY DIFFRACTION99.384
3.232-3.3450.246560.218890X-RAY DIFFRACTION100
3.345-3.4710.253460.203875X-RAY DIFFRACTION100
3.471-3.6130.205410.18838X-RAY DIFFRACTION99.8864
3.613-3.7730.184510.176795X-RAY DIFFRACTION100
3.773-3.9560.228460.161772X-RAY DIFFRACTION100
3.956-4.170.153350.145728X-RAY DIFFRACTION100
4.17-4.4220.146430.117684X-RAY DIFFRACTION100
4.422-4.7260.143330.114658X-RAY DIFFRACTION100
4.726-5.1020.174460.127611X-RAY DIFFRACTION100
5.102-5.5860.217320.137554X-RAY DIFFRACTION100
5.586-6.240.178400.15512X-RAY DIFFRACTION100
6.24-7.1960.217160.157460X-RAY DIFFRACTION100
7.196-8.7890.235110.162399X-RAY DIFFRACTION100
8.789-12.3280.201110.164321X-RAY DIFFRACTION100
12.328-68.50.20720.38190X-RAY DIFFRACTION96

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