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- PDB-8zup: Crystal structure of the F99S/M153T/V163A/T203V/E222Q variant of ... -

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Basic information

Entry
Database: PDB / ID: 8zup
TitleCrystal structure of the F99S/M153T/V163A/T203V/E222Q variant of GFP at pH 8.5
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / GREEN FLUORESCENT PROTEIN
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: 1.2 Å
AuthorsTakeda, R. / Takeda, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Takeda Science Foundation Japan
Gimpu fund from Kyoto University Japan
CitationJournal: Sci Rep / Year: 2024
Title: Structural characterization of green fluorescent protein in the I-state.
Authors: Takeda, R. / Tsutsumi, E. / Okatsu, K. / Fukai, S. / Takeda, K.
History
DepositionJun 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8903
Polymers25,8411
Non-polymers492
Water8,881493
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-6 kcal/mol
Surface area10330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.696, 62.273, 68.429
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Green fluorescent protein


Mass: 25841.000 Da / Num. of mol.: 1 / Mutation: F99S,M153T,V163A,T203V,E222Q
Source method: isolated from a genetically manipulated source
Details: Q80R was caused by a PCR error in the early study (Chalfie, M. et al., Science, 1994)
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42212
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 308 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PEG 4000, magnesium chloride, MES-NaOH buffer (pH 5.0)

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Data collection

DiffractionMean temperature: 15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.7 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.2→46.06 Å / Num. obs: 68191 / % possible obs: 99.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 8.45 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.155 / Rrim(I) all: 0.168 / Net I/σ(I): 6.45
Reflection shellResolution: 1.2→1.27 Å / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 2.15 / Num. unique obs: 10818 / CC1/2: 0.845 / Rrim(I) all: 0.606 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→46.06 Å / SU ML: 0.1061 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.9302
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1729 3412 5 %
Rwork0.139 64767 -
obs0.1407 68179 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.22 Å2
Refinement stepCycle: LAST / Resolution: 1.2→46.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1821 0 2 493 2316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082061
X-RAY DIFFRACTIONf_angle_d1.05772820
X-RAY DIFFRACTIONf_chiral_restr0.1306
X-RAY DIFFRACTIONf_plane_restr0.0089371
X-RAY DIFFRACTIONf_dihedral_angle_d13.1233814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.220.2231500.18592611X-RAY DIFFRACTION98.33
1.22-1.240.24981280.19362677X-RAY DIFFRACTION99.29
1.24-1.250.24711490.18962633X-RAY DIFFRACTION99.78
1.25-1.280.23111440.18642641X-RAY DIFFRACTION99.25
1.28-1.30.21791280.17842686X-RAY DIFFRACTION99.79
1.3-1.320.23521370.17662662X-RAY DIFFRACTION99.57
1.32-1.350.24891360.17642671X-RAY DIFFRACTION99.5
1.35-1.370.21621490.17672662X-RAY DIFFRACTION99.61
1.37-1.40.2281360.16822688X-RAY DIFFRACTION99.93
1.4-1.440.22831450.16772652X-RAY DIFFRACTION99.68
1.44-1.470.19791390.16022680X-RAY DIFFRACTION99.82
1.47-1.510.18941530.14832681X-RAY DIFFRACTION99.82
1.51-1.560.19041530.13792672X-RAY DIFFRACTION99.86
1.56-1.610.18371330.13832695X-RAY DIFFRACTION99.93
1.61-1.660.16951510.13212673X-RAY DIFFRACTION99.93
1.66-1.730.17751510.12972711X-RAY DIFFRACTION100
1.73-1.810.15631410.13192707X-RAY DIFFRACTION99.89
1.81-1.90.14741550.12562675X-RAY DIFFRACTION99.93
1.91-2.020.13181280.11022753X-RAY DIFFRACTION100
2.02-2.180.1561210.11572737X-RAY DIFFRACTION100
2.18-2.40.14671520.132739X-RAY DIFFRACTION100
2.4-2.750.15681220.13342781X-RAY DIFFRACTION100
2.75-3.460.14391560.12562766X-RAY DIFFRACTION100
3.46-46.060.1661550.13332914X-RAY DIFFRACTION99.74

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