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- PDB-8jls: Crystal structure of the Green fluorescent protein SET203EF223DA2... -

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Basic information

Entry
Database: PDB / ID: 8jls
TitleCrystal structure of the Green fluorescent protein SET203EF223DA227 variant at pH 6.0
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / bioimaging / Sensor. GFP
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsShin, S.C.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of the Green fluorescent protein SET203EF223DA227 variant at pH 6.0
Authors: Shin, S.C.
History
DepositionJun 2, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,9541
Polymers26,9541
Non-polymers00
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.190, 46.438, 121.856
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 Green fluorescent protein


Mass: 26954.344 Da / Num. of mol.: 1
Mutation: F64L,Q80R,S147D,N149Q,V163A,S175G,S202F,Q204E,A206T,F223D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 1.94 Å3/Da / Density % sol: 36.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M acetate pH 6.0, 25% (w/v) PEG 1500, 30% (w/v) MPD

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 35914 / % possible obs: 98.7 % / Redundancy: 11.3 % / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.036 / Rrim(I) all: 0.13 / Χ2: 1.466 / Net I/σ(I): 5.6 / Num. measured all: 404720
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.45-1.57.40.39432710.8020.9440.1430.4210.51291.9
1.5-1.569.30.35235060.9110.9760.1150.3710.60598.5
1.56-1.6310.10.3235390.9370.9840.1010.3360.74799
1.63-1.7210.60.28135810.9620.990.0860.2940.91399.2
1.72-1.8311.20.23635700.9690.9920.070.2461.11199.4
1.83-1.9711.90.18935850.9850.9960.0550.1971.4199.4
1.97-2.1712.50.15536150.9910.9980.0440.1611.67199.8
2.17-2.48130.13436650.9910.9980.0380.1391.7899.8
2.48-3.1213.30.11336870.9950.9990.0310.1171.964100
3.12-5012.70.09938950.9950.9990.0280.1032.72499.8

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→43.39 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 17.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2031 2000 5.58 %
Rwork0.1805 --
obs0.1818 35859 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→43.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1803 0 0 246 2049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061844
X-RAY DIFFRACTIONf_angle_d1.042493
X-RAY DIFFRACTIONf_dihedral_angle_d6.689242
X-RAY DIFFRACTIONf_chiral_restr0.099266
X-RAY DIFFRACTIONf_plane_restr0.008327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.490.25571310.24312214X-RAY DIFFRACTION93
1.49-1.530.26651410.22332394X-RAY DIFFRACTION98
1.53-1.570.25991390.20612352X-RAY DIFFRACTION99
1.57-1.620.21711420.19442395X-RAY DIFFRACTION99
1.62-1.680.22421400.18282377X-RAY DIFFRACTION99
1.68-1.750.21191410.1762401X-RAY DIFFRACTION100
1.75-1.830.18611430.1772405X-RAY DIFFRACTION99
1.83-1.930.20751430.17792427X-RAY DIFFRACTION100
1.93-2.050.21241420.16982400X-RAY DIFFRACTION100
2.05-2.20.17811450.16622451X-RAY DIFFRACTION100
2.2-2.430.21891440.18132440X-RAY DIFFRACTION100
2.43-2.780.20691460.18592470X-RAY DIFFRACTION100
2.78-3.50.1961480.17852502X-RAY DIFFRACTION100
3.5-43.390.18171550.17242631X-RAY DIFFRACTION100

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