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- PDB-8jll: Crystal structure of the Green fluorescent protein SEA227D varian... -

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Basic information

Entry
Database: PDB / ID: 8jll
TitleCrystal structure of the Green fluorescent protein SEA227D variant at pH 9.5
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: 2.69 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 SEA227D variant at pH 9.5
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
B: Green fluorescent protein
C: Green fluorescent protein
D: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)108,0104
Polymers108,0104
Non-polymers00
Water00
1
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,0021
Polymers27,0021
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,0021
Polymers27,0021
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,0021
Polymers27,0021
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,0021
Polymers27,0021
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.210, 80.964, 179.884
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: 27002.430 Da / Num. of mol.: 4
Mutation: F64L,Q80R,S147D,N149Q,V163A,S175G,S202F,Q204T,A206T,A227D
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
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: 2.72 Å3/Da / Density % sol: 54.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M CHES pH 9.5, 0.2M sodium chloride, 1.26M ammonium sulfate

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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: Nov 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 30706 / % possible obs: 97.4 % / Redundancy: 7.1 % / CC1/2: 0.936 / CC star: 0.983 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.076 / Rrim(I) all: 0.226 / Χ2: 0.635 / Net I/σ(I): 2.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.7-2.83.50.4528350.5660.850.2280.5090.34391.8
2.8-2.9150.4629130.5710.8530.20.5050.33894.5
2.91-3.046.10.42330460.7860.9380.1660.4570.38398.3
3.04-3.26.80.36930920.8760.9670.1370.3950.45898.8
3.2-3.46.90.33130610.890.970.1250.3560.48998.5
3.4-3.667.60.26330530.9590.9890.0940.280.58597.6
3.66-4.038.40.22231240.970.9920.0750.2350.68899
4.03-4.628.60.17130940.9840.9960.0580.1810.8798.2
4.62-5.819.10.16531960.9840.9960.0550.1750.80699.6
5.81-6.318.70.13132920.9910.9980.0440.1390.83597.7

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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: 2.69→48.19 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 26.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2823 1988 6.65 %
Rwork0.2005 --
obs0.2058 29913 94.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.69→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7192 0 0 0 7192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017360
X-RAY DIFFRACTIONf_angle_d1.1699948
X-RAY DIFFRACTIONf_dihedral_angle_d8.091960
X-RAY DIFFRACTIONf_chiral_restr0.0581060
X-RAY DIFFRACTIONf_plane_restr0.0081300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.760.38161220.2731769X-RAY DIFFRACTION86
2.76-2.840.35351250.27381802X-RAY DIFFRACTION87
2.84-2.920.36241430.26181960X-RAY DIFFRACTION94
2.92-3.010.33461430.2481950X-RAY DIFFRACTION95
3.01-3.120.32711430.21331962X-RAY DIFFRACTION96
3.12-3.250.31041380.2062012X-RAY DIFFRACTION96
3.25-3.390.25641450.20231988X-RAY DIFFRACTION97
3.4-3.570.27811360.19251971X-RAY DIFFRACTION94
3.57-3.80.30411500.19572042X-RAY DIFFRACTION98
3.8-4.090.27091460.17462051X-RAY DIFFRACTION98
4.09-4.50.22641410.15482070X-RAY DIFFRACTION97
4.5-5.150.24651500.15222052X-RAY DIFFRACTION98
5.15-6.490.2221520.20222119X-RAY DIFFRACTION98
6.49-48.190.28831540.22182177X-RAY DIFFRACTION96

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