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

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Basic information

Entry
Database: PDB / ID: 5vik
TitleCrystal structure of monomeric near-infrared fluorescent protein miRFP703
Componentsnear-infrared fluorescent protein miRFP703
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 / Phytochrome, central region / PAS fold-2 / PAS fold / 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 / Phytochrome, central region / PAS fold-2 / PAS fold / 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: 1.35 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 / Refinement description / Category: citation / citation_author / software
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name
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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: near-infrared fluorescent protein miRFP703
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1402
Polymers34,5571
Non-polymers5831
Water5,044280
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)36.319, 52.821, 64.622
Angle α, β, γ (deg.)90.000, 92.530, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein near-infrared fluorescent protein miRFP703


Mass: 34556.941 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


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
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: 1.79 Å3/Da / Density % sol: 31.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.08M Na Citrate pH 5.0, 24% v/v Jeffamine ED-2001 pH 7.0 0.4% n-octyl-beta-D-glucopyranoside

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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: 1.35→29.93 Å / Num. obs: 53575 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.033 / Rrim(I) all: 0.063 / Χ2: 0.898 / Net I/σ(I): 13.6 / Num. measured all: 197471
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.35-1.43.30.3680.8680.2410.4410.7999.9
1.4-1.453.60.2760.9320.170.3250.828100
1.45-1.523.70.1980.9650.1210.2320.851100
1.52-1.63.70.1360.9820.0830.1590.881100
1.6-1.73.70.1010.990.0610.1180.923100
1.7-1.833.70.0710.9940.0430.0830.974100
1.83-2.023.80.0510.9960.0310.060.977100
2.02-2.313.80.0490.9960.0290.0580.892100
2.31-2.913.80.0530.9960.0320.0620.894100
2.91-503.70.0470.9940.0280.0550.94499.5

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XTQ

4xtq


Resolution: 1.35→29.93 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.979 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.055
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.174 1666 3.1 %RANDOM
Rwork0.1215 ---
obs0.1232 51889 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 101.64 Å2 / Biso mean: 20.485 Å2 / Biso min: 8.87 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å2-0 Å2-1.03 Å2
2---1.63 Å2-0 Å2
3---0.29 Å2
Refinement stepCycle: final / Resolution: 1.35→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2299 0 43 281 2623
Biso mean--12.54 31.82 -
Num. residues----296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192555
X-RAY DIFFRACTIONr_bond_other_d0.0060.022484
X-RAY DIFFRACTIONr_angle_refined_deg2.32423494
X-RAY DIFFRACTIONr_angle_other_deg1.44835709
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0265328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.79422.182110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51715431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8841528
X-RAY DIFFRACTIONr_chiral_restr0.1290.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212954
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02599
X-RAY DIFFRACTIONr_rigid_bond_restr7.34335039
X-RAY DIFFRACTIONr_sphericity_free23.238578
X-RAY DIFFRACTIONr_sphericity_bonded12.35455172
LS refinement shellResolution: 1.351→1.386 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 120 -
Rwork0.186 3729 -
all-3849 -
obs--98.44 %

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