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

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Basic information

Entry
Database: PDB / ID: 9fen
TitleLSSmOrange (P1) - Directionality of Optical Properties of Fluorescent Proteins
ComponentsnowGFP crystallized in Space Group C2
KeywordsFLUORESCENT PROTEIN
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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: nowGFP crystallized in Space Group C2


Theoretical massNumber of molelcules
Total (without water)27,8811
Polymers27,8811
Non-polymers00
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-3 kcal/mol
Surface area10560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.900, 51.480, 55.630
Angle α, β, γ (deg.)90.00, 100.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein nowGFP crystallized in Space Group C2


Mass: 27881.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.83 Å3/Da / Density % sol: 56.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20 % w/v Polyethylene glycol 6,000 100 mM tri-Sodium citrate

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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 PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. obs: 85128 / % possible obs: 97.9 % / Redundancy: 2.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.081 / Net I/σ(I): 9.98
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.56-1.651.551136530.2771.8331
1.65-1.770.89128570.5231.0511
1.77-1.910.45120610.8250.531
1.91-2.090.233110230.9350.2771
2.09-2.340.136101090.9780.161
2.34-2.70.08289250.9910.0971
2.7-3.30.04675380.9980.0541
3.3-4.660.02957800.9990.0341
4.66-500.02431820.9990.0281

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→42.89 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.009 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19935 1003 2.5 %RANDOM
Rwork0.17044 ---
obs0.17116 39620 98.51 %-
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: 35.826 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å2-0.33 Å2
2---0.11 Å2-0 Å2
3---0.35 Å2
Refinement stepCycle: 1 / Resolution: 1.6→42.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 0 218 2028
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131947
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171792
X-RAY DIFFRACTIONr_angle_refined_deg1.8411.6742657
X-RAY DIFFRACTIONr_angle_other_deg1.3881.6054179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3775254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.07324.706102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78615338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.794156
X-RAY DIFFRACTIONr_chiral_restr0.0730.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022255
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02428
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_it2.353.523938
X-RAY DIFFRACTIONr_mcbond_other2.3483.52937
X-RAY DIFFRACTIONr_mcangle_it3.0235.2751176
X-RAY DIFFRACTIONr_mcangle_other3.0235.2791177
X-RAY DIFFRACTIONr_scbond_it3.7893.8791009
X-RAY DIFFRACTIONr_scbond_other3.783.8811009
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6585.671466
X-RAY DIFFRACTIONr_long_range_B_refined7.13141.7612160
X-RAY DIFFRACTIONr_long_range_B_other7.06441.052103
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 72 -
Rwork0.338 2879 -
obs--97.81 %

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