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- PDB-9fel: LSSmCherry1 - Directionality of Optical Properties of Fluorescent... -

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Basic information

Entry
Database: PDB / ID: 9fel
TitleLSSmCherry1 - Directionality of Optical Properties of Fluorescent Proteins
ComponentsPAmCherry1 protein
KeywordsFLUORESCENT PROTEIN
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / ACETATE ION / BETA-MERCAPTOETHANOL / PAmCherry1 protein
Function and homology information
Biological speciesDiscosoma sp. (sea anemone)
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 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 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: PAmCherry1 protein
L: PAmCherry1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1037
Polymers60,6962
Non-polymers4075
Water6,593366
1
A: PAmCherry1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6775
Polymers30,3481
Non-polymers3294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
L: PAmCherry1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4262
Polymers30,3481
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.540, 107.980, 58.730
Angle α, β, γ (deg.)90.00, 103.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PAmCherry1 protein


Mass: 30347.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. (sea anemone) / Gene: PAmCherry, PAmCherry1 / Production host: Escherichia coli (E. coli) / References: UniProt: D1MPT3
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 100mM Bis-Tris 200mM lithium sulfate 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 76295 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.121 / Rrim(I) all: 0.131 / Net I/σ(I): 9.94
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.5-1.591.909123030.4332.0671
1.59-1.71.222115470.5831.3321
1.7-1.840.679107720.8520.7371
1.84-2.010.33899170.9650.3651
2.01-2.250.19289650.9850.2071
2.25-2.590.13279370.9930.1421
2.59-3.170.07766960.9970.0841
3.17-4.470.04552310.9980.0491
4.47-500.04129270.9990.0441

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→39.2 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.402 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21321 2100 2.8 %RANDOM
Rwork0.18913 ---
obs0.18979 74175 99.96 %-
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: 21.607 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å2-0 Å2-1.17 Å2
2---0.63 Å2-0 Å2
3---0.22 Å2
Refinement stepCycle: 1 / Resolution: 1.5→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3457 0 22 366 3845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133646
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173361
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.6634913
X-RAY DIFFRACTIONr_angle_other_deg1.4311.5917816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1085446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.8922.611203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84515644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2131520
X-RAY DIFFRACTIONr_chiral_restr0.0890.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024123
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02809
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_it1.821.9811736
X-RAY DIFFRACTIONr_mcbond_other1.811.9791734
X-RAY DIFFRACTIONr_mcangle_it2.5172.9632170
X-RAY DIFFRACTIONr_mcangle_other2.5162.9642171
X-RAY DIFFRACTIONr_scbond_it3.4062.3931910
X-RAY DIFFRACTIONr_scbond_other3.4062.3931911
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0673.4312735
X-RAY DIFFRACTIONr_long_range_B_refined7.29623.9643913
X-RAY DIFFRACTIONr_long_range_B_other6.12523.573836
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
Rfree0.379 154 -
Rwork0.37 5444 -
obs--99.96 %

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