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- PDB-9feo: LSSmOrange (P1) - Directionality of Optical Properties of Fluores... -

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Basic information

Entry
Database: PDB / ID: 9feo
TitleLSSmOrange (P1) - Directionality of Optical Properties of Fluorescent Proteins
ComponentsmOrange
KeywordsFLUORESCENT PROTEIN
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / metal ion binding / mOrange
Function and homology information
Biological speciesDiscosoma sp. (sea anemone)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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

Downloads & links

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Assembly

Deposited unit
A: mOrange
C: mOrange


Theoretical massNumber of molelcules
Total (without water)55,7292
Polymers55,7292
Non-polymers00
Water4,161231
1
A: mOrange


Theoretical massNumber of molelcules
Total (without water)27,8641
Polymers27,8641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: mOrange


Theoretical massNumber of molelcules
Total (without water)27,8641
Polymers27,8641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.955, 51.536, 53.892
Angle α, β, γ (deg.)95.69, 90.01, 105.68
Int Tables number1
Space group name H-MP1

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Components

#1: Protein mOrange


Mass: 27864.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: D0VWW2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.31 Å3/Da / Density % sol: 46.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 100mM MES, 5 % w/v Polyethylene glycol 8000 40 % v/v 2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Apr 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 33363 / % possible obs: 91.4 % / Redundancy: 3.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.046 / Rrim(I) all: 0.094 / Χ2: 0.95 / Net I/σ(I): 10
Reflection shellResolution: 1.9→1.94 Å / % possible obs: 52.6 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.407 / Num. measured all: 2036 / Num. unique obs: 1309 / CC1/2: 0.755 / Rpim(I) all: 0.348 / Rrim(I) all: 0.537 / Χ2: 1.03 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
CrysalisProdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→26.32 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.906 / SU B: 4.672 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26201 1608 4.8 %RANDOM
Rwork0.20353 ---
obs0.2063 31726 91.28 %-
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: 22.198 Å2
Baniso -1Baniso -2Baniso -3
1--2.55 Å20.71 Å20.06 Å2
2--1.48 Å2-0.41 Å2
3---0.52 Å2
Refinement stepCycle: 1 / Resolution: 1.9→26.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3435 0 0 231 3666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133566
X-RAY DIFFRACTIONr_bond_other_d0.0030.0173313
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.6874808
X-RAY DIFFRACTIONr_angle_other_deg1.3571.6087705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8035432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.1923.315178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.18215637
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.131516
X-RAY DIFFRACTIONr_chiral_restr0.0820.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023973
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02779
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_it1.8832.1311707
X-RAY DIFFRACTIONr_mcbond_other1.8832.131706
X-RAY DIFFRACTIONr_mcangle_it2.6263.1882131
X-RAY DIFFRACTIONr_mcangle_other2.6253.192132
X-RAY DIFFRACTIONr_scbond_it2.9312.4521859
X-RAY DIFFRACTIONr_scbond_other2.9312.4521859
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5323.552673
X-RAY DIFFRACTIONr_long_range_B_refined5.85924.9773877
X-RAY DIFFRACTIONr_long_range_B_other5.82724.8323837
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 63 -
Rwork0.274 1401 -
obs--53.28 %

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