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- PDB-8zus: Crystal structure of the F99S/M153T/V163A/T203V variant of GFP at... -

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Basic information

Entry
Database: PDB / ID: 8zus
TitleCrystal structure of the F99S/M153T/V163A/T203V variant of GFP at pH 7.5
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
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)25,8913
Polymers25,8421
Non-polymers492
Water9,350519
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 area10320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.720, 62.236, 68.343
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: 25841.984 Da / Num. of mol.: 1 / Mutation: F99S,M153T,V163A,T203V
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.: 519 / 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: 41.06 %
Crystal growTemperature: 308 K / Method: vapor diffusion, sitting drop
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: Feb 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.2→46.02 Å / Num. obs: 68343 / % possible obs: 99.9 % / Redundancy: 6.73 % / Biso Wilson estimate: 9.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Rrim(I) all: 0.118 / Net I/σ(I): 10
Reflection shellResolution: 1.2→1.27 Å / Redundancy: 6.34 % / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 2.12 / Num. unique obs: 10858 / CC1/2: 0.841 / Rrim(I) all: 0.668 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→46.02 Å / SU ML: 0.1197 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.6978
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1653 3419 5 %
Rwork0.1327 64908 -
obs0.1343 68327 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.94 Å2
Refinement stepCycle: LAST / Resolution: 1.2→46.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1823 0 2 519 2344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00662138
X-RAY DIFFRACTIONf_angle_d0.98442939
X-RAY DIFFRACTIONf_chiral_restr0.093316
X-RAY DIFFRACTIONf_plane_restr0.0076392
X-RAY DIFFRACTIONf_dihedral_angle_d13.2876864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.220.24731500.21982598X-RAY DIFFRACTION98.14
1.22-1.230.24561310.20622685X-RAY DIFFRACTION99.93
1.23-1.250.24031500.18872643X-RAY DIFFRACTION99.96
1.25-1.270.2341450.18252673X-RAY DIFFRACTION99.93
1.27-1.30.2051270.17572698X-RAY DIFFRACTION100
1.3-1.320.19681370.15782665X-RAY DIFFRACTION100
1.32-1.350.20581380.15872692X-RAY DIFFRACTION99.96
1.35-1.370.17851490.14972672X-RAY DIFFRACTION99.96
1.37-1.40.19791340.14712688X-RAY DIFFRACTION99.96
1.4-1.440.18461470.14842665X-RAY DIFFRACTION99.93
1.44-1.470.19391390.14522677X-RAY DIFFRACTION100
1.47-1.510.18161560.13982686X-RAY DIFFRACTION100
1.51-1.560.18311520.13892675X-RAY DIFFRACTION99.96
1.56-1.610.17811340.12722705X-RAY DIFFRACTION100
1.61-1.660.151490.12142687X-RAY DIFFRACTION100
1.66-1.730.17441520.1192711X-RAY DIFFRACTION100
1.73-1.810.14321390.11662709X-RAY DIFFRACTION100
1.81-1.90.14331580.1182677X-RAY DIFFRACTION100
1.9-2.020.14341270.11262755X-RAY DIFFRACTION100
2.02-2.180.13421210.11532743X-RAY DIFFRACTION100
2.18-2.40.13771530.12242738X-RAY DIFFRACTION100
2.4-2.750.15441210.13092779X-RAY DIFFRACTION100
2.75-3.460.13961570.12282773X-RAY DIFFRACTION100
3.46-46.020.17731530.12832914X-RAY DIFFRACTION99.64

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