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

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Basic information

Entry
Database: PDB / ID: 9fgi
TitleLSSmOrange (P1) - Directionality of Optical Properties of Fluorescent Proteins
ComponentsnowGFP
KeywordsFLUORESCENT PROTEIN
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 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
B: nowGFP


Theoretical massNumber of molelcules
Total (without water)55,0742
Polymers55,0742
Non-polymers00
Water3,081171
1
A: nowGFP


Theoretical massNumber of molelcules
Total (without water)27,5371
Polymers27,5371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: nowGFP


Theoretical massNumber of molelcules
Total (without water)27,5371
Polymers27,5371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.260, 51.390, 195.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein nowGFP


Mass: 27537.072 Da / Num. of mol.: 2
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.: 171 / 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: 46.79 %
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: Jul 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 51138 / % possible obs: 99.1 % / Redundancy: 13.1 % / Biso Wilson estimate: 38.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.108 / Net I/σ(I): 16.6
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.77-1.882.7479700.4972.331
1.88-21.54538080.4050.671
2-2.160.86534840.6810.381
2.16-2.370.46431490.860.221
2.37-2.650.24327720.9450.2841
2.65-3.060.12324030.9870.1431
3.06-3.740.05419540.9970.0621
3.74-5.280.03414460.9990.0391
5.28-500.03221310.9990.0361

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→49.59 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.08 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23958 2101 4.1 %RANDOM
Rwork0.19874 ---
obs0.20041 49037 99.09 %-
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: 41.139 Å2
Baniso -1Baniso -2Baniso -3
1-2.33 Å2-0 Å20 Å2
2---0.63 Å2-0 Å2
3----1.7 Å2
Refinement stepCycle: 1 / Resolution: 1.77→49.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3633 0 0 171 3804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0133721
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173481
X-RAY DIFFRACTIONr_angle_refined_deg2.1281.6685023
X-RAY DIFFRACTIONr_angle_other_deg1.4031.6048064
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.225454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.63624.239184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.1615647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7751512
X-RAY DIFFRACTIONr_chiral_restr0.0870.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024193
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02815
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_it4.1414.0111822
X-RAY DIFFRACTIONr_mcbond_other4.1274.0091821
X-RAY DIFFRACTIONr_mcangle_it5.0036.0042271
X-RAY DIFFRACTIONr_mcangle_other5.0086.0072272
X-RAY DIFFRACTIONr_scbond_it5.94.561899
X-RAY DIFFRACTIONr_scbond_other5.8994.5621900
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.5526.5942752
X-RAY DIFFRACTIONr_long_range_B_refined9.96546.1493857
X-RAY DIFFRACTIONr_long_range_B_other9.9846.0763837
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.814 Å
RfactorNum. reflection% reflection
Rfree0.342 148 -
Rwork0.364 3446 -
obs--96.33 %

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