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- PDB-9ffi: mScarlet (SG C5) - Directionality of Optical Properties of Fluore... -

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Basic information

Entry
Database: PDB / ID: 9ffi
TitlemScarlet (SG C5) - Directionality of Optical Properties of Fluorescent Proteins
ComponentsmScarlet
KeywordsFLUORESCENT PROTEIN
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMyskova, J. / Brynda, J. / Lazar, J.
Funding support Czech Republic, 2items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicCZ.02.1.01/0.0/0.0/16_019/0000729 Czech Republic
Czech Science Foundation23-05983S Czech Republic
Citation
Journal: To Be Published
Title: Directionality of Optical Properties of Fluorescent Proteins
Authors: Myskova, J. / Brynda, J. / Khoroshyy, P. / Lazar, J.
#1: Journal: To Be Published
Title: Directional optical properties of fluorescent proteins
Authors: Myskova, J. / Lazar, J.
History
DepositionMay 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 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: mScarlet
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4322
Polymers30,3371
Non-polymers951
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-6 kcal/mol
Surface area10070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.892, 45.098, 58.294
Angle α, β, γ (deg.)90.00, 101.78, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

21A-483-

HOH

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Components

#1: Protein mScarlet


Mass: 30337.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MVSKGEAVIK EFMRFKVHME GSMNGHEFEI EGEGEGRPYE GTQTAKLKVT KGGPLPFSWD ILSPQFMYG(NRQ)S RAFTKHPADI PDYYKQSFPE GFKWERVMNF EDGGAVTVTQ DTSLEDGTLI YKVKLRGTNF PPDGPVMQKK TMGWEASTER LYPEDGVLKG ...Details: MVSKGEAVIK EFMRFKVHME GSMNGHEFEI EGEGEGRPYE GTQTAKLKVT KGGPLPFSWD ILSPQFMYG(NRQ)S RAFTKHPADI PDYYKQSFPE GFKWERVMNF EDGGAVTVTQ DTSLEDGTLI YKVKLRGTNF PPDGPVMQKK TMGWEASTER LYPEDGVLKG DIKMALRLKD GGRYLADFKT TYKAKKPVQM PGAYNVDRKL DITSHNEDYT VVEQYERSEG RHSTGGMDEL YK
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 35 % v/v Polyethylene glycol 400 70 mM Sodium acetate 140 mM Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91814 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91814 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 34204 / % possible obs: 99.5 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.076 / Net I/σ(I): 10.92
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.5-1.541.2625150.5311.4711
1.54-1.581.03424510.6161.2061
1.58-1.630.79423800.7130.9321
1.63-1.680.65923410.730.7791
1.68-1.730.55222330.8310.6411
1.73-1.790.41221800.9350.4781
1.79-1.860.30521130.9510.3541
1.86-1.940.20920220.9780.2421
1.94-2.020.15319300.9910.1781
2.02-2.120.11518590.9910.1341
2.12-2.240.09717750.9940.1131
2.24-2.370.07816840.9940.0931
2.37-2.540.06915710.9950.081
2.54-2.740.05614710.9970.0651
2.74-30.04313370.9980.051
3-3.350.03512080.9980.041
3.35-3.870.02910860.9980.0351
3.87-4.740.0249190.9990.0291
4.74-6.710.0237250.9990.0271
6.71-500.0274040.9990.0311

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→41.1 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.459 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22352 1706 5 %RANDOM
Rwork0.18967 ---
obs0.19142 32419 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.085 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å20 Å2-1.32 Å2
2--0.73 Å20 Å2
3---1.47 Å2
Refinement stepCycle: 1 / Resolution: 1.5→41.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 5 84 1873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131891
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171724
X-RAY DIFFRACTIONr_angle_refined_deg1.8681.6712562
X-RAY DIFFRACTIONr_angle_other_deg1.4631.5914010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5065236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.17822.17106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32715328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6311512
X-RAY DIFFRACTIONr_chiral_restr0.0860.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022157
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02427
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_it2.1792.965904
X-RAY DIFFRACTIONr_mcbond_other2.1692.964903
X-RAY DIFFRACTIONr_mcangle_it2.8264.4391131
X-RAY DIFFRACTIONr_mcangle_other2.8294.441132
X-RAY DIFFRACTIONr_scbond_it3.6913.31987
X-RAY DIFFRACTIONr_scbond_other3.6653.301983
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2784.8161416
X-RAY DIFFRACTIONr_long_range_B_refined5.92633.541969
X-RAY DIFFRACTIONr_long_range_B_other5.91533.4181958
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 123 -
Rwork0.441 2344 -
obs--97.94 %

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