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- PDB-7a7y: rsGreen0.7-F145Q in the green-on state -

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Basic information

Entry
Database: PDB / ID: 7a7y
TitlersGreen0.7-F145Q in the green-on state
ComponentsrsGreen0.7-F145Q
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 / NITRATE ION / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 Å
AuthorsDe Zitter, E. / Dedecker, P. / Van Meervelt, L.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO) 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 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: rsGreen0.7-F145Q
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7122
Polymers30,6501
Non-polymers621
Water9,116506
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint0 kcal/mol
Surface area11260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.197, 51.268, 48.583
Angle α, β, γ (deg.)90.000, 101.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein rsGreen0.7-F145Q


Mass: 30650.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Production host: Escherichia coli (E. coli) / Variant (production host): JM109 / References: UniProt: A0A059PIQ0
#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.88 Å3/Da / Density % sol: 34.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 200 mM KNO3 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.97→46.32 Å / Num. obs: 129948 / % possible obs: 96.8 % / Redundancy: 3.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.041 / Rrim(I) all: 0.076 / Net I/σ(I): 10.9 / Num. measured all: 405332 / Scaling rejects: 38
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
0.97-0.992.10.457864541180.7450.3730.5941.862.3
5.31-46.323.50.0630008630.9850.0380.07122.399.7

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.23data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
PHASER2.7.16phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XOW

4xow


Resolution: 0.97→46.317 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 12.86
RfactorNum. reflection% reflection
Rfree0.1417 6465 4.98 %
Rwork0.1253 --
obs0.1261 129902 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.16 Å2 / Biso mean: 14.4188 Å2 / Biso min: 2.18 Å2
Refinement stepCycle: final / Resolution: 0.97→46.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1892 0 4 506 2402
Biso mean--35.82 29.14 -
Num. residues----239
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
0.97-0.9810.22931240.2467250159
0.981-0.99260.21281380.2216303171
0.9926-1.00470.23811640.2118375688
1.0047-1.01740.19762180.1932418799
1.0174-1.03080.18262120.1741419899
1.0308-1.04490.19382510.1585418799
1.0449-1.05980.15932340.15674210100
1.0598-1.07570.21942250.187419699
1.0757-1.09250.15882280.13864205100
1.0925-1.11040.13432230.1224420899
1.1104-1.12950.13732560.133418499
1.1295-1.15010.15242250.11744213100
1.1501-1.17220.12262360.1136420399
1.1722-1.19610.11752060.1124227100
1.1961-1.22210.15722120.1226423799
1.2221-1.25060.13191940.1244242100
1.2506-1.28180.11942410.1126422599
1.2818-1.31650.12372080.128420499
1.3165-1.35520.13762390.1103421099
1.3552-1.3990.12652300.1111418799
1.399-1.4490.12672260.11144250100
1.449-1.5070.13041850.11014274100
1.507-1.57560.13262150.10474238100
1.5756-1.65870.12392160.10724254100
1.6587-1.76260.11862110.11554262100
1.7626-1.89870.13482210.12024260100
1.8987-2.08980.14082280.1222421899
2.0898-2.39210.11612470.1221422999
2.3921-3.01380.14232260.13034299100
3.0138-46.3170.16272260.1232434299

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