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- PDB-7a8j: rsGreen0.7-K206A-H148V in the green-on state -

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Basic information

Entry
Database: PDB / ID: 7a8j
TitlersGreen0.7-K206A-H148V in the green-on state
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / Reversible photoswitchable 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 / Resolution: 1.85 Å
AuthorsDe Zitter, E. / Dedecker, P. / Van Meervelt, L.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders Belgium
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Structure-Function Dataset Reveals Environment Effects within a Fluorescent Protein Model System*.
Authors: De Zitter, E. / Hugelier, S. / Duwe, S. / Vandenberg, W. / Tebo, A.G. / Van Meervelt, L. / Dedecker, P.
History
DepositionAug 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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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)30,6642
Polymers30,5721
Non-polymers921
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint1 kcal/mol
Surface area10500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.616, 140.616, 73.004
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-535-

HOH

21A-585-

HOH

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Components

#1: Protein Green fluorescent protein /


Mass: 30572.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: gfp / Production host: Escherichia coli (E. coli) / Variant (production host): JM109 / References: UniProt: A0A059PIQ0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

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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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM MES pH 6.5 25 % PEG 550 mme 10 mM ZnSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 18, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→46.76 Å / Num. obs: 23673 / % possible obs: 100 % / Redundancy: 10.2 % / Biso Wilson estimate: 27.48 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.017 / Rrim(I) all: 0.053 / Net I/σ(I): 28.4 / Num. measured all: 241673
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.85-1.8910.30.66414430.9320.2170.699100
9.06-46.769.90.01822410.0060.0299.1

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.23data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHENIX1.11phasing
RefinementResolution: 1.85→40.592 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2315 1181 4.99 %
Rwork0.189 22483 -
obs0.1912 23664 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.52 Å2 / Biso mean: 34.5845 Å2 / Biso min: 12.48 Å2
Refinement stepCycle: final / Resolution: 1.85→40.592 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1825 0 6 232 2063
Biso mean--51.43 40.69 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091948
X-RAY DIFFRACTIONf_angle_d0.9562647
X-RAY DIFFRACTIONf_chiral_restr0.07286
X-RAY DIFFRACTIONf_plane_restr0.006352
X-RAY DIFFRACTIONf_dihedral_angle_d10.6541568
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8501-1.93430.36571380.296127992937
1.9343-2.03630.30691320.256727872919
2.0363-2.16380.2911500.239227912941
2.1638-2.33090.29241540.230827762930
2.3309-2.56540.26991480.216328312979
2.5654-2.93660.23641390.210428062945
2.9366-3.69940.24181500.172428122962
3.6994-40.60210.16911700.142328813051

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