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- PDB-7a8n: rsGreen0.7-K206A-N205L in the green-on state -

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Basic information

Entry
Database: PDB / ID: 7a8n
TitlersGreen0.7-K206A-N205L 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: 2.1 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
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)30,6101
Polymers30,6101
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.728, 140.728, 73.246
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-340-

HOH

21A-460-

HOH

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Components

#1: Protein Green fluorescent protein


Mass: 30610.393 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM HEPES pH 7.5 25 % PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 28, 2017
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.1→46.845 Å / Num. obs: 16005 / % possible obs: 98.3 % / Redundancy: 20.3 % / Biso Wilson estimate: 39.99 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.013 / Rrim(I) all: 0.058 / Net I/σ(I): 33.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.1620.30.71313070.9640.1620.73197.5
8.91-46.8417.10.02623910.0070.02699.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHENIX1.11refinement
PDB_EXTRACT3.24data extraction
PHENIX1.11phasing
RefinementResolution: 2.1→46.845 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 31.06
RfactorNum. reflection% reflection
Rfree0.2575 794 4.96 %
Rwork0.2084 --
obs0.2109 15995 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.11 Å2 / Biso mean: 44.87 Å2 / Biso min: 23.04 Å2
Refinement stepCycle: final / Resolution: 2.1→46.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 0 0 190 2003
Biso mean---46.76 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021923
X-RAY DIFFRACTIONf_angle_d0.5242610
X-RAY DIFFRACTIONf_chiral_restr0.044281
X-RAY DIFFRACTIONf_plane_restr0.003344
X-RAY DIFFRACTIONf_dihedral_angle_d9.4981537
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1001-2.23170.32851250.27942514263997
2.2317-2.4040.34051300.28322473260397
2.404-2.64590.32181150.27192537265298
2.6459-3.02870.28071380.24832516265498
3.0287-3.81560.25241440.19942538268299
3.8156-46.85660.22021420.16582623276599

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