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- PDB-8zut: Crystal structure of the F99S/M153T/V163A variant of GFP at pH 8.5 -

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Basic information

Entry
Database: PDB / ID: 8zut
TitleCrystal structure of the F99S/M153T/V163A 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: 1.48 Å
AuthorsTakeda, R. / Tsutsumi, E. / 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
Revision 1.1Jun 18, 2025Group: Database references / Category: pdbx_related_exp_data_set

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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)25,8933
Polymers25,8441
Non-polymers492
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-6 kcal/mol
Surface area10270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.536, 62.347, 67.758
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Green fluorescent protein


Mass: 25843.957 Da / Num. of mol.: 1 / Mutation: F99S,M153T,V163A
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.: 402 / 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: 2.07 Å3/Da / Density % sol: 40.44 %
Crystal growTemperature: 308 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 4000, magnesium chloride, Tris-HCl buffer (pH 8.5)

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Data collection

DiffractionMean temperature: 16 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: Jul 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.48→45.88 Å / Num. obs: 36341 / % possible obs: 99.9 % / Redundancy: 6.56 % / Biso Wilson estimate: 12.65 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.152 / Rrim(I) all: 0.165 / Net I/σ(I): 9.01
Reflection shellResolution: 1.48→1.57 Å / Rmerge(I) obs: 1.972 / Num. unique obs: 3504 / CC1/2: 0.053 / Rrim(I) all: 2.789

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→45.88 Å / SU ML: 0.1587 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.1615
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1973 1812 4.99 %
Rwork0.161 34518 -
obs0.1628 36330 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.89 Å2
Refinement stepCycle: LAST / Resolution: 1.48→45.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1818 0 2 402 2222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00881945
X-RAY DIFFRACTIONf_angle_d1.01232644
X-RAY DIFFRACTIONf_chiral_restr0.0994286
X-RAY DIFFRACTIONf_plane_restr0.0087346
X-RAY DIFFRACTIONf_dihedral_angle_d12.9463740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.520.29321500.25332589X-RAY DIFFRACTION99.89
1.52-1.570.25621420.23022619X-RAY DIFFRACTION99.93
1.57-1.620.26611370.21252614X-RAY DIFFRACTION99.96
1.62-1.670.2411440.19722623X-RAY DIFFRACTION100
1.67-1.740.26281470.20112611X-RAY DIFFRACTION99.96
1.74-1.820.21861390.18452639X-RAY DIFFRACTION99.96
1.82-1.920.20561460.16252615X-RAY DIFFRACTION100
1.92-2.040.20111170.15022655X-RAY DIFFRACTION100
2.04-2.190.18671270.15882686X-RAY DIFFRACTION100
2.19-2.410.16681410.15282654X-RAY DIFFRACTION99.96
2.41-2.760.20741190.15292699X-RAY DIFFRACTION99.96
2.76-3.480.16371560.14392698X-RAY DIFFRACTION100
3.48-45.880.17661470.13832816X-RAY DIFFRACTION99.23

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