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- PDB-7a7t: rsGreenF partially in the green-off state -

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Basic information

Entry
Database: PDB / ID: 7a7t
TitlersGreenF 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 / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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 23, 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)30,6721
Polymers30,6721
Non-polymers00
Water5,314295
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 area10340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.617, 62.263, 48.460
Angle α, β, γ (deg.)90.000, 90.360, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Green fluorescent protein


Mass: 30672.420 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) / Strain (production host): JM109 / References: UniProt: A0A059PIQ0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.19 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM MIB pH 4.0 25 % PEG 1500

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Data collection

DiffractionMean temperature: 100 K
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: 1.58→48.46 Å / Num. obs: 30705 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 20.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.022 / Rrim(I) all: 0.058 / Net I/σ(I): 17.2 / Num. measured all: 203376
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.58-1.615.90.66714920.840.3050.73799.9
8.65-48.465.40.0352050.9980.0160.03999.2

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHENIX1.11refinement
PDB_EXTRACT3.24data extraction
PHENIX1.11phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→48.459 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.96
RfactorNum. reflection% reflection
Rfree0.1967 1563 5.1 %
Rwork0.1621 --
obs0.1638 30676 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.85 Å2 / Biso mean: 24.6875 Å2 / Biso min: 11.19 Å2
Refinement stepCycle: final / Resolution: 1.58→48.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1807 0 0 295 2102
Biso mean---36.69 -
Num. residues----228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072054
X-RAY DIFFRACTIONf_angle_d0.9042807
X-RAY DIFFRACTIONf_chiral_restr0.065298
X-RAY DIFFRACTIONf_plane_restr0.005376
X-RAY DIFFRACTIONf_dihedral_angle_d7.7912000
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5801-1.63110.35981390.340226252764
1.6311-1.68940.24991390.232426122751
1.6894-1.7570.21061540.186826352789
1.757-1.8370.21631330.173226332766
1.837-1.93390.2321420.17726362778
1.9339-2.0550.22031190.162726832802
2.055-2.21370.18171380.160626602798
2.2137-2.43650.21581560.16326192775
2.4365-2.7890.21121580.170926432801
2.789-3.51370.19991260.15126722798
3.5137-48.48180.15561590.137726952854

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