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

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Basic information

Entry
Database: PDB / ID: 8jlu
TitleCrystal structure of the Green fluorescent protein SET203EF223DA227 variant at pH 8.5
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: 2.09 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 8.5
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)107,8174
Polymers107,8174
Non-polymers00
Water6,936385
1
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,9541
Polymers26,9541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,9541
Polymers26,9541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,9541
Polymers26,9541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,9541
Polymers26,9541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.834, 46.295, 146.593
Angle α, β, γ (deg.)90.00, 93.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Green fluorescent protein


Mass: 26954.344 Da / Num. of mol.: 4
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.: 385 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris pH 8.5, 0.1M Magnesium chloride, 25% (w/v) PEG 33

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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: 2.09→50 Å / Num. obs: 47276 / % possible obs: 84.4 % / Redundancy: 4.2 % / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.039 / Rrim(I) all: 0.093 / Χ2: 1.192 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.1-2.182.70.23441810.8250.9510.1410.2750.76675.5
2.18-2.262.80.21742740.8660.9630.1290.2540.81177.1
2.26-2.3730.19943770.9050.9750.1140.2310.88778.5
2.37-2.493.30.17644810.9320.9820.0980.2030.980.9
2.49-2.653.60.15446160.9560.9890.0810.1750.97382.7
2.65-2.8540.13547130.9710.9930.0670.1521.07284.3
2.85-3.144.50.10447840.9880.9970.0480.1161.18485.7
3.14-3.595.20.08149570.9930.9980.0350.0891.3188.3
3.59-4.525.70.06552370.9950.9990.0280.0711.41692.5
4.52-5.025.90.06356560.9950.9990.0270.0691.49397.2

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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: 2.09→49.23 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 22.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2454 2001 4.23 %
Rwork0.193 --
obs0.1952 47273 83.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→49.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7204 0 0 385 7589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077368
X-RAY DIFFRACTIONf_angle_d1.0499964
X-RAY DIFFRACTIONf_dihedral_angle_d9.146968
X-RAY DIFFRACTIONf_chiral_restr0.061064
X-RAY DIFFRACTIONf_plane_restr0.0081308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.150.33581050.23982453X-RAY DIFFRACTION64
2.15-2.20.27021190.22162907X-RAY DIFFRACTION75
2.2-2.270.29931360.2232997X-RAY DIFFRACTION79
2.27-2.340.29561380.20653011X-RAY DIFFRACTION78
2.34-2.430.29721290.20813067X-RAY DIFFRACTION80
2.43-2.520.23751390.20263161X-RAY DIFFRACTION83
2.52-2.640.2671450.21263168X-RAY DIFFRACTION82
2.64-2.780.25581360.21663264X-RAY DIFFRACTION84
2.78-2.950.28681510.22743255X-RAY DIFFRACTION84
2.95-3.180.26671530.20433343X-RAY DIFFRACTION87
3.18-3.50.24571530.20323421X-RAY DIFFRACTION88
3.5-40.21261550.17123537X-RAY DIFFRACTION91
4-5.040.19511630.14833750X-RAY DIFFRACTION95
5.04-49.230.22391790.18143938X-RAY DIFFRACTION97

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