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- PDB-9fes: mCherry - Directionality of Optical Properties of Fluorescent Proteins -

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Basic information

Entry
Database: PDB / ID: 9fes
TitlemCherry - Directionality of Optical Properties of Fluorescent Proteins
ComponentsMCHERRY
KeywordsFLUORESCENT PROTEIN
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / MCHERRY
Function and homology information
Biological speciesDiscosoma (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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 21, 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

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Assembly

Deposited unit
A: MCHERRY


Theoretical massNumber of molelcules
Total (without water)30,6331
Polymers30,6331
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.686, 42.294, 56.683
Angle α, β, γ (deg.)90.00, 108.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MCHERRY


Mass: 30633.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma (sea anemone) / Gene: mCherry / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4D6FVK6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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 % sol: 29.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M TRIS hydrochloride, 0.2 M Magnesium chloride hexahydrate, 30% w/v Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. obs: 23804 / % possible obs: 95.1 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.029 / Rrim(I) all: 0.077 / Net I/σ(I): 12.2
Reflection shellResolution: 1.66→1.72 Å / % possible obs: 68.3 % / Redundancy: 5 % / Rmerge(I) obs: 1.14 / Num. measured all: 8236 / Num. unique obs: 1642 / CC1/2: 0.713 / Rpim(I) all: 0.546 / Rrim(I) all: 1.272 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→44.42 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.988 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24295 1180 5 %RANDOM
Rwork0.19711 ---
obs0.19933 22617 94.9 %-
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: 30.227 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20 Å2-3.75 Å2
2--0.62 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.66→44.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1740 0 0 92 1832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131784
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171646
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.6732401
X-RAY DIFFRACTIONr_angle_other_deg1.4011.6043813
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6395217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.17323.06888
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4315306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.862158
X-RAY DIFFRACTIONr_chiral_restr0.1010.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022007
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02400
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_it2.5522.945874
X-RAY DIFFRACTIONr_mcbond_other2.5162.942873
X-RAY DIFFRACTIONr_mcangle_it3.5434.4041089
X-RAY DIFFRACTIONr_mcangle_other3.5424.4071090
X-RAY DIFFRACTIONr_scbond_it3.9013.375910
X-RAY DIFFRACTIONr_scbond_other3.9013.377911
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9034.8741312
X-RAY DIFFRACTIONr_long_range_B_refined7.18833.6591860
X-RAY DIFFRACTIONr_long_range_B_other7.12133.4691848
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.495 56 -
Rwork0.452 1053 -
obs--59.98 %

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