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- PDB-7a7v: rsGreen1-K206A partially in the green-off state -

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Basic information

Entry
Database: PDB / ID: 7a7v
TitlersGreen1-K206A partially in the green-off 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 / DI(HYDROXYETHYL)ETHER / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 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 1.2Nov 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8483
Polymers30,6491
Non-polymers1982
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint2 kcal/mol
Surface area10160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.550, 73.550, 114.377
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-593-

HOH

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Components

#1: Protein Green fluorescent protein


Mass: 30649.318 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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 3.02 Å3/Da / Density % sol: 59.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Bis-tris pH 5.5 200 mM (NH4)2SO4 16 % 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, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2→47.343 Å / Num. obs: 21948 / % possible obs: 100 % / Redundancy: 25.8 % / Biso Wilson estimate: 36.67 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.011 / Rrim(I) all: 0.054 / Net I/σ(I): 38.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.0527.20.61615850.9870.120.628100
8.94-47.3419.60.02631410.0060.02799.6

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.6.2data scaling
PHENIX1.11refinement
PDB_EXTRACT3.24data extraction
PHENIX1.11phasing
RefinementResolution: 2→47.343 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1936 1141 5.22 %
Rwork0.1592 20729 -
obs0.1611 21870 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.38 Å2 / Biso mean: 41.1197 Å2 / Biso min: 24.25 Å2
Refinement stepCycle: final / Resolution: 2→47.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 13 237 2037
Biso mean--60.21 50.6 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071918
X-RAY DIFFRACTIONf_angle_d0.8762604
X-RAY DIFFRACTIONf_chiral_restr0.061277
X-RAY DIFFRACTIONf_plane_restr0.005345
X-RAY DIFFRACTIONf_dihedral_angle_d19.9851121
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
2-2.09110.22881400.17825352675
2.0911-2.20130.22121320.168325312663
2.2013-2.33920.21781540.164325122666
2.3392-2.51980.23321420.168325672709
2.5198-2.77340.25411270.178825822709
2.7734-3.17460.21411360.174226012737
3.1746-3.99940.20131620.150326182780
3.9994-47.35650.14851480.148427832931

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