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- PDB-7a8e: rsGreen0.7-K206A-F165W partially in the green-off state -

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Basic information

Entry
Database: PDB / ID: 7a8e
TitlersGreen0.7-K206A-F165W 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 / Resolution: 2.2 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 20, 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)30,6501
Polymers30,6501
Non-polymers00
Water2,216123
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 area10510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.744, 140.744, 72.897
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-337-

HOH

21A-412-

HOH

31A-416-

HOH

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Components

#1: Protein Green fluorescent protein


Mass: 30650.373 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.: 123 / 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: 54.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM HEPES pH 7.5 25 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 9, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.2→46.76 Å / Num. obs: 14148 / % possible obs: 100 % / Redundancy: 20.1 % / Biso Wilson estimate: 44.29 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.013 / Rrim(I) all: 0.06 / Net I/σ(I): 32.1 / Num. measured all: 284967
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.2719.30.6572339112110.9640.1540.6755.399.9
9.07-46.7617.20.0338712250.9990.0070.03186.199.4

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Processing

Software
NameVersionClassification
PHENIX1.11refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
PHENIX1.11phasing
RefinementResolution: 2.2→46.756 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 30.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2613 714 5.05 %
Rwork0.205 13423 -
obs0.2078 14137 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.12 Å2 / Biso mean: 50.6243 Å2 / Biso min: 25.96 Å2
Refinement stepCycle: final / Resolution: 2.2→46.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1821 0 0 123 1944
Biso mean---50.41 -
Num. residues----229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021938
X-RAY DIFFRACTIONf_angle_d0.5422632
X-RAY DIFFRACTIONf_chiral_restr0.044280
X-RAY DIFFRACTIONf_plane_restr0.003346
X-RAY DIFFRACTIONf_dihedral_angle_d8.4961981
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2001-2.370.3691260.304626582784
2.37-2.60840.36461420.281126532795
2.6084-2.98580.36741510.275126712822
2.9858-3.76160.291410.208726862827
3.7616-46.76690.18331540.155127552909

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