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- PDB-8q6w: LSSmOrange - Directionality of Optical Properties of Fluorescent ... -

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Basic information

Entry
Database: PDB / ID: 8q6w
TitleLSSmOrange - Directionality of Optical Properties of Fluorescent Proteins
ComponentsmOrange
KeywordsFLUORESCENT PROTEIN
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / metal ion binding
Similarity search - Function
Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / mOrange
Similarity search - Component
Biological speciesDiscosoma sp. (sea anemone)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.43 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
DepositionAug 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2024Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9009
Polymers27,8641
Non-polymers1,0368
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-20 kcal/mol
Surface area10260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.090, 68.090, 41.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 1 molecules A

#1: Protein mOrange


Mass: 27864.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: D0VWW2

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Non-polymers , 5 types, 156 molecules

#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 100 mM Sodium acetate 50 % v/v Polyethylene glycol 400 200 mM Lithium sulfate

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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: Mar 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 41808 / % possible obs: 99.6 % / Redundancy: 9.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.084 / Net I/σ(I): 14.55
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.4-1.481.29566330.6081.3911
1.48-1.590.78363870.8690.8231
1.59-1.710.48459380.9440.511
1.71-1.880.26854450.9840.2821
1.88-2.10.13449440.9950.1411
2.1-2.420.08943590.9970.0941
2.42-2.960.06136810.9990.0641
2.96-4.170.04328380.9990.0451
4.17-500.03915830.9990.0411

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
CrysalisProdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→34.04 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.243 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18076 1966 5 %RANDOM
Rwork0.13355 ---
obs0.13587 37349 99.92 %-
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: 21.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-0.48 Å2-0 Å2
2---0.95 Å2-0 Å2
3---3.09 Å2
Refinement stepCycle: 1 / Resolution: 1.43→34.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1744 0 62 148 1954
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131864
X-RAY DIFFRACTIONr_bond_other_d0.0090.0171763
X-RAY DIFFRACTIONr_angle_refined_deg1.8521.6852498
X-RAY DIFFRACTIONr_angle_other_deg1.4971.6054102
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.415220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.9323.07791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64715327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.936159
X-RAY DIFFRACTIONr_chiral_restr0.0940.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022011
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02395
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_it2.9951.914866
X-RAY DIFFRACTIONr_mcbond_other2.991.908864
X-RAY DIFFRACTIONr_mcangle_it3.812.8661078
X-RAY DIFFRACTIONr_mcangle_other3.8092.871079
X-RAY DIFFRACTIONr_scbond_it4.7012.5998
X-RAY DIFFRACTIONr_scbond_other4.682.5987
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8752.51399
X-RAY DIFFRACTIONr_long_range_B_refined5.16731970
X-RAY DIFFRACTIONr_long_range_B_other5.12231950
X-RAY DIFFRACTIONr_rigid_bond_restr4.52431819
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.43→1.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 147 -
Rwork0.297 2798 -
obs--99.49 %

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