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- PDB-5viq: Crystal structure of monomeric near-infrared fluorescent protein ... -

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Basic information

Entry
Database: PDB / ID: 5viq
TitleCrystal structure of monomeric near-infrared fluorescent protein miRFP709
Componentsmonomeric near-infrared fluorescent protein miRFP709
KeywordsFLUORESCENT PROTEIN / near-infrared fluorescent protein / biliverdin / phytochrome / RpBphP1
Function / homology
Function and homology information


detection of visible light / photoreceptor activity / regulation of DNA-templated transcription / ATP binding
Similarity search - Function
Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. ...Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / 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 fold / PAS fold / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
BILIVERDINE IX ALPHA / Putative PAS/PAC sensor protein
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsPletnev, S.
CitationJournal: Chem Sci / Year: 2017
Title: Designing brighter near-infrared fluorescent proteins: insights from structural and biochemical studies.
Authors: Baloban, M. / Shcherbakova, D.M. / Pletnev, S. / Pletnev, V.Z. / Lagarias, J.C. / Verkhusha, V.V.
History
DepositionApr 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: monomeric near-infrared fluorescent protein miRFP709
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1882
Polymers34,6051
Non-polymers5831
Water5,134285
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.266, 52.860, 64.625
Angle α, β, γ (deg.)90.000, 92.700, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein monomeric near-infrared fluorescent protein miRFP709


Mass: 34604.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Production host: Escherichia coli (E. coli) / References: UniProt: B3Q7C0*PLUS
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H34N4O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O

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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: 1.79 Å3/Da / Density % sol: 31.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.16 M MgCl2, 0.08 M Tris-HCl pH 8.5, 20% w/v PEG 3350, 3.2% 2,2,2-trifluoroethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.34→27.54 Å / Num. obs: 55190 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.033 / Rrim(I) all: 0.065 / Χ2: 0.935 / Net I/σ(I): 15.4 / Num. measured all: 199515
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.34-1.393.20.5170.8290.3360.620.83297.6
1.39-1.443.50.4180.8890.260.4940.85999.9
1.44-1.513.60.2920.9440.180.3440.928100
1.51-1.593.60.1940.9740.1190.2280.984100
1.59-1.693.70.1380.9850.0840.1621.03100
1.69-1.823.70.0960.9920.0580.1121.022100
1.82-23.70.070.9940.0420.0820.981100
2-2.293.70.0670.9930.0410.0790.945100
2.29-2.893.70.0590.9950.0350.0680.893100
2.89-303.70.0440.9960.0270.0510.85398.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XTQ

4xtq


Resolution: 1.34→27.54 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.556 / SU ML: 0.046 / SU R Cruickshank DPI: 0.0571 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.058
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1877 1701 3.1 %RANDOM
Rwork0.1357 ---
obs0.1373 53465 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 96.02 Å2 / Biso mean: 23.532 Å2 / Biso min: 9.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å2-0 Å2-2.43 Å2
2---1.28 Å2-0 Å2
3----0.18 Å2
Refinement stepCycle: final / Resolution: 1.34→27.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2303 0 43 285 2631
Biso mean--13.4 33.09 -
Num. residues----296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0192553
X-RAY DIFFRACTIONr_bond_other_d0.0090.022487
X-RAY DIFFRACTIONr_angle_refined_deg2.34823489
X-RAY DIFFRACTIONr_angle_other_deg1.50935715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.785327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.64822.018109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79915433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1511528
X-RAY DIFFRACTIONr_chiral_restr0.1360.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212946
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02603
X-RAY DIFFRACTIONr_rigid_bond_restr8.7835040
X-RAY DIFFRACTIONr_sphericity_free21.01574
X-RAY DIFFRACTIONr_sphericity_bonded13.25755179
LS refinement shellResolution: 1.335→1.37 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 107 -
Rwork0.266 3721 -
all-3828 -
obs--93.48 %

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