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- PDB-7a7n: rsGreen0.7b in the green-off state -

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Basic information

Entry
Database: PDB / ID: 7a7n
TitlersGreen0.7b 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: 1.2 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)30,6851
Polymers30,6851
Non-polymers00
Water6,485360
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 area10390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.866, 61.568, 105.117
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Green fluorescent protein


Mass: 30685.439 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.: 360 / 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: 1.99 Å3/Da / Density % sol: 38.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM MMT pH 5.0 25 % PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 19, 2016
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→39.974 Å / Num. obs: 63701 / % possible obs: 97.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 10.38 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.028 / Rrim(I) all: 0.054 / Net I/σ(I): 14.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.2-1.223.60.42229670.8440.2490.49292.7
6.57-39.973.40.0254670.9990.0150.02997.8

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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: 1.2→39.974 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.11
RfactorNum. reflection% reflection
Rfree0.1704 3196 5.02 %
Rwork0.1375 --
obs0.1392 63636 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.33 Å2 / Biso mean: 16.2448 Å2 / Biso min: 0.38 Å2
Refinement stepCycle: final / Resolution: 1.2→39.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1820 0 0 360 2180
Biso mean---27.79 -
Num. residues----228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082174
X-RAY DIFFRACTIONf_angle_d1.0162983
X-RAY DIFFRACTIONf_chiral_restr0.082311
X-RAY DIFFRACTIONf_plane_restr0.007409
X-RAY DIFFRACTIONf_dihedral_angle_d23.068840
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.21790.25341490.20022450259992
1.2179-1.2370.24051310.19182495262693
1.237-1.25720.22331380.18672524266295
1.2572-1.27890.25781110.1992616272796
1.2789-1.30220.25391450.18442534267996
1.3022-1.32720.2131520.1682625277797
1.3272-1.35430.2141160.16672595271197
1.3543-1.38380.23541510.1712585273696
1.3838-1.4160.18541480.1462550269897
1.416-1.45140.18551280.14552642277098
1.4514-1.49060.17511370.13452598273597
1.4906-1.53450.18311430.13512629277297
1.5345-1.5840.17321430.12822649279298
1.584-1.64060.16371490.12582636278598
1.6406-1.70630.18561330.1242650278398
1.7063-1.7840.15751460.12552667281398
1.784-1.8780.13921270.12132695282298
1.878-1.99570.15511380.12342624276297
1.9957-2.14980.1571240.12422679280398
2.1498-2.36610.17531250.12932675280098
2.3661-2.70840.17281480.13192716286498
2.7084-3.4120.14051550.13262725288098
3.412-39.99620.15561590.13642881304098

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