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- PDB-8jl5: Crystal structure of the Green fluorescent protein SEA227D varian... -

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Basic information

Entry
Database: PDB / ID: 8jl5
TitleCrystal structure of the Green fluorescent protein SEA227D variant at pH 4.5
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: 1.8 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 4.5
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

Downloads & links

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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
Water15,889882
1
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,0021
Polymers27,0021
Non-polymers00
Water181
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
Water181
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
Water181
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
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.935, 82.947, 180.132
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 882 / 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: 2.69 Å3/Da / Density % sol: 54.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1M Citric acid pH 4.5, 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 298 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: 1.8→50 Å / Num. obs: 102810 / % possible obs: 99.2 % / Redundancy: 11.1 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.041 / Rrim(I) all: 0.146 / Χ2: 1.025 / Net I/σ(I): 4.3 / Num. measured all: 1136537
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.8-1.8680.461100370.6280.8780.1650.4910.43398.3
1.86-1.9490.427100880.7890.9390.1430.4520.53598.6
1.94-2.039.70.373101680.8860.9690.120.3920.6698.8
2.03-2.1310.30.325101930.9330.9820.10.340.78599.2
2.13-2.2710.80.285101660.9590.9890.0860.2980.87799.2
2.27-2.4411.30.239102320.9770.9940.0710.250.95999.4
2.44-2.6911.90.195102980.9860.9960.0560.2031.05899.5
2.69-3.0812.50.15103750.9920.9980.0420.1561.19399.7
3.08-3.8813.40.103104390.9960.9990.0280.1071.44999.8
3.88-5013.30.086108140.9970.9990.0240.091.61799.6

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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: 1.8→41.47 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 20 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 1999 1.95 %
Rwork0.1853 --
obs0.186 102744 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→41.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7233 0 0 882 8115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087400
X-RAY DIFFRACTIONf_angle_d1.03210000
X-RAY DIFFRACTIONf_dihedral_angle_d6.7966
X-RAY DIFFRACTIONf_chiral_restr0.0641067
X-RAY DIFFRACTIONf_plane_restr0.0081306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.33031370.27996885X-RAY DIFFRACTION96
1.84-1.890.26261390.25097067X-RAY DIFFRACTION98
1.89-1.950.27191420.22917111X-RAY DIFFRACTION99
1.95-2.010.23981410.20597077X-RAY DIFFRACTION99
2.01-2.080.24821410.19387110X-RAY DIFFRACTION99
2.08-2.170.21341410.18537163X-RAY DIFFRACTION99
2.17-2.260.21121430.17977152X-RAY DIFFRACTION99
2.26-2.380.22431420.17617196X-RAY DIFFRACTION99
2.38-2.530.23951430.18017202X-RAY DIFFRACTION100
2.53-2.730.22141430.18817206X-RAY DIFFRACTION99
2.73-30.23911450.18867275X-RAY DIFFRACTION100
3-3.440.21091450.17377293X-RAY DIFFRACTION100
3.44-4.330.19661470.1597406X-RAY DIFFRACTION100
4.33-41.470.18841500.1767602X-RAY DIFFRACTION99

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