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- PDB-7a8d: rsGreen0.7-K206A-F165W partially in the green-on state -

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Basic information

Entry
Database: PDB / ID: 7a8d
TitlersGreen0.7-K206A-F165W partially 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 / MOLECULAR REPLACEMENT / Resolution: 1.65 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

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Assembly

Deposited unit
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)30,6501
Polymers30,6501
Non-polymers00
Water4,900272
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 area10590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.570, 140.570, 72.972
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-409-

HOH

21A-499-

HOH

31A-524-

HOH

41A-558-

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.: 272 / 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: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 200 mM NH4F 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 18, 2017
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→46.74 Å / Num. obs: 33227 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 25.18 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.014 / Rrim(I) all: 0.046 / Net I/σ(I): 27.7 / Num. measured all: 371129 / Scaling rejects: 4
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
1.65-1.6810.80.7481752516240.8940.2380.7853.2100
9.04-46.7410.60.04224382290.9970.0140.04580.599.4

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Processing

Software
NameVersionClassification
PHENIX1.11refinement
XDSdata reduction
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
PHENIX1.11phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→46.742 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.68
RfactorNum. reflection% reflection
Rfree0.2191 1593 4.8 %
Rwork0.1919 --
obs0.1933 33219 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.65 Å2 / Biso mean: 34.8412 Å2 / Biso min: 13.8 Å2
Refinement stepCycle: final / Resolution: 1.65→46.742 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1836 0 0 272 2108
Biso mean---43.43 -
Num. residues----233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062050
X-RAY DIFFRACTIONf_angle_d0.9052797
X-RAY DIFFRACTIONf_chiral_restr0.062294
X-RAY DIFFRACTIONf_plane_restr0.005374
X-RAY DIFFRACTIONf_dihedral_angle_d10.3731994
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
1.6501-1.70330.31021330.270428622995
1.7033-1.76420.30581510.269428593010
1.7642-1.83490.30391400.266328402980
1.8349-1.91840.30741280.262928773005
1.9184-2.01950.29551640.253628483012
2.0195-2.1460.29721310.243128642995
2.146-2.31170.3071580.234128523010
2.3117-2.54430.26951440.223128753019
2.5443-2.91250.24421410.205728833024
2.9125-3.66920.20161490.165529063055
3.6692-46.76080.13321540.135729603114

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