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

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Basic information

Entry
Database: PDB / ID: 9feq
TitleLSSmOrange (P1) - Directionality of Optical Properties of Fluorescent Proteins
ComponentswasCFP crystallized in SG P212121
KeywordsFLUORESCENT PROTEIN
Function / homologyDI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION
Function and homology information
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: wasCFP crystallized in SG P212121
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0098
Polymers28,4041
Non-polymers6057
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-22 kcal/mol
Surface area10360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.950, 62.080, 68.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein wasCFP crystallized in SG P212121


Mass: 28403.949 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)

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Non-polymers , 6 types, 195 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.92 Å3/Da / Density % sol: 35.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 40 % v/v Polyethylene glycol 300 100 mM MES 200 mM Calcium acetate

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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: Jan 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 36428 / % possible obs: 99.7 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.146 / Rrim(I) all: 0.161 / Net I/σ(I): 8.41
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.85-1.962.84958720.3373.1561
1.96-2.11.26155520.631.3831
2.1-2.260.76151520.8080.8371
2.26-2.480.48247450.9050.5321
2.48-2.770.28342980.9680.311
2.77-3.20.14137790.9920.1561
3.2-3.910.07332140.9970.081
3.91-5.510.0524430.9980.0561
5.51-500.03613730.9990.041

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→46.1 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.836 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21447 1458 5 %RANDOM
Rwork0.17745 ---
obs0.17931 27763 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: 19.891 Å2
Baniso -1Baniso -2Baniso -3
1--1.67 Å2-0 Å2-0 Å2
2---0.61 Å20 Å2
3---2.28 Å2
Refinement stepCycle: 1 / Resolution: 1.6→46.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 34 188 2009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131931
X-RAY DIFFRACTIONr_bond_other_d0.0070.0171814
X-RAY DIFFRACTIONr_angle_refined_deg1.9631.6732613
X-RAY DIFFRACTIONr_angle_other_deg1.4521.6044213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5145245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52524.58396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66415332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.468156
X-RAY DIFFRACTIONr_chiral_restr0.0890.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022194
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02425
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_it1.7251.826926
X-RAY DIFFRACTIONr_mcbond_other1.7241.823925
X-RAY DIFFRACTIONr_mcangle_it2.5212.7311162
X-RAY DIFFRACTIONr_mcangle_other2.522.7351163
X-RAY DIFFRACTIONr_scbond_it2.9342.2011005
X-RAY DIFFRACTIONr_scbond_other2.9162.191003
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4753.1341439
X-RAY DIFFRACTIONr_long_range_B_refined6.70622.5162077
X-RAY DIFFRACTIONr_long_range_B_other6.5321.9292021
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
Rfree0.374 101 -
Rwork0.326 1953 -
obs--95.09 %

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