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- PDB-7a8b: rsGreen0.7-K206A-F145S partially in the green-on state -

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Basic information

Entry
Database: PDB / ID: 7a8b
TitlersGreen0.7-K206A-F145S 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 / Resolution: 1.55 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 1.1Mar 17, 2021Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2May 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 1.3Nov 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


Theoretical massNumber of molelcules
Total (without water)30,5511
Polymers30,5511
Non-polymers00
Water4,594255
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 area10790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.548, 139.548, 72.864
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-436-

HOH

21A-483-

HOH

31A-527-

HOH

41A-539-

HOH

51A-553-

HOH

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Components

#1: Protein Green fluorescent protein


Mass: 30551.244 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.: 255 / 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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM MES pH 6.0 14 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 22, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.55→46.51 Å / Num. obs: 38704 / % possible obs: 98.5 % / Redundancy: 9.9 % / Biso Wilson estimate: 27.71 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.015 / Rrim(I) all: 0.046 / Net I/σ(I): 22.2 / Num. measured all: 384350 / Scaling rejects: 9
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
1.55-1.589.20.6821740718850.8730.2340.7212.797.6
8.49-46.518.90.0323852680.9990.0110.0325499.4

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
PHENIX1.11phasing
RefinementResolution: 1.55→46.513 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2321 1945 5.03 %
Rwork0.1932 36754 -
obs0.1951 38699 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118 Å2 / Biso mean: 36.554 Å2 / Biso min: 16.62 Å2
Refinement stepCycle: final / Resolution: 1.55→46.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1835 0 0 255 2090
Biso mean---44.6 -
Num. residues----234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062072
X-RAY DIFFRACTIONf_angle_d0.8542834
X-RAY DIFFRACTIONf_chiral_restr0.056300
X-RAY DIFFRACTIONf_plane_restr0.005383
X-RAY DIFFRACTIONf_dihedral_angle_d10.4341990
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.58880.2971310.28772582271397
1.5888-1.63170.28621360.2752550268697
1.6317-1.67980.29481350.26462605274097
1.6798-1.7340.29841190.26942598271797
1.734-1.7960.34211680.27212542271098
1.796-1.86790.29981230.26722640276398
1.8679-1.95290.27311420.25982595273798
1.9529-2.05580.28781430.24592622276599
2.0558-2.18460.28971460.23462620276699
2.1846-2.35330.27381350.23722650278599
2.3533-2.59010.25221320.21742631276399
2.5901-2.96490.24941270.20892696282399
2.9649-3.73520.24991560.167626732829100
3.7352-46.53370.14941520.135927502902100

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