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- PDB-9f03: mRhubarb720-WT -

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Basic information

Entry
Database: PDB / ID: 9f03
TitlemRhubarb720-WT
ComponentsmRhubarb720 fluorescent protein
KeywordsFLUORESCENT PROTEIN / monomeric rhubarb720 / mRhubarb720 / near-IR / Biliverdin / Biliverdin XI-Alpha / Imaging / Raman spectroscopy
Function / homology
Function and homology information


regulation of DNA-templated transcription
Similarity search - Function
PAS fold-2 / PAS fold / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / PAS domain superfamily
Similarity search - Domain/homology
Chem-LBV / Near-infrared fluorescent protein
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsAksakal, O. / Rizkallah, P.J. / Warren, A. / Lipka-Lloyd, M. / Jones, D.D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
CitationJournal: To Be Published
Title: Monomeric rhubarb fluorescent protein
Authors: Aksakal, O. / Rizkallah, P.J. / Jones, D.D.
History
DepositionApr 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mRhubarb720 fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8822
Polymers33,2961
Non-polymers5861
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-13 kcal/mol
Surface area14060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.845, 58.845, 185.883
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein mRhubarb720 fluorescent protein / mRhubarb720 fluorescent protein / Near-infrared fluorescent protein


Mass: 33296.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: iRFP / Production host: Escherichia coli (E. coli) / References: UniProt: G1FNL7
#2: Chemical ChemComp-LBV / 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid / 2(R),3(E)- PHYTOCHROMOBILIN


Mass: 585.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H37N4O6 / Feature type: SUBJECT OF INVESTIGATION
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: 2.42 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 293 K / Method: batch mode
Details: Buffer: 0.1 M MMT (DL-Malic acid, MES monohydrate) Precipitant: 25 % w/v PEG 1500 pH: 5.0

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Data collection

DiffractionMean temperature: 200 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: VMXi / Wavelength: 0.58136 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.58136 Å / Relative weight: 1
ReflectionResolution: 3.3→27.43 Å / Num. obs: 5072 / % possible obs: 95.1 % / Redundancy: 4.2 % / CC1/2: 0.971 / Rmerge(I) obs: 0.334 / Rpim(I) all: 0.17 / Rrim(I) all: 0.377 / Χ2: 1.36 / Net I/σ(I): 4.8
Reflection shellResolution: 3.3→3.57 Å / % possible obs: 90.7 % / Redundancy: 2.9 % / Rmerge(I) obs: 1.645 / Num. measured all: 2786 / Num. unique obs: 953 / CC1/2: 0.315 / Rpim(I) all: 1.007 / Rrim(I) all: 1.946 / Χ2: 1.05 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→27.43 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.907 / SU B: 63.719 / SU ML: 0.892 / Cross valid method: THROUGHOUT / ESU R Free: 0.749 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30885 261 5.2 %RANDOM
Rwork0.22494 ---
obs0.23 4779 93.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.969 Å2
Baniso -1Baniso -2Baniso -3
1-2.47 Å2-0 Å2-0 Å2
2--2.47 Å2-0 Å2
3----4.93 Å2
Refinement stepCycle: 1 / Resolution: 3.3→27.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2339 0 43 0 2382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132437
X-RAY DIFFRACTIONr_bond_other_d0.0040.0152313
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.6483321
X-RAY DIFFRACTIONr_angle_other_deg1.0991.5725301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.6245303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.30119.857140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.49715380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8671524
X-RAY DIFFRACTIONr_chiral_restr0.0520.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022817
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02561
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.1368.7761215
X-RAY DIFFRACTIONr_mcbond_other8.1248.7711214
X-RAY DIFFRACTIONr_mcangle_it13.00813.1321517
X-RAY DIFFRACTIONr_mcangle_other13.00413.1391518
X-RAY DIFFRACTIONr_scbond_it7.4439.5931222
X-RAY DIFFRACTIONr_scbond_other7.4399.5961223
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.30714.0981805
X-RAY DIFFRACTIONr_long_range_B_refined19.544152786
X-RAY DIFFRACTIONr_long_range_B_other19.541152787
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.303→3.388 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 14 -
Rwork0.41 300 -
obs--84.18 %

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