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- PDB-7a7w: rsGreen0.7-F145M partially in the green-on state -

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Basic information

Entry
Database: PDB / ID: 7a7w
TitlersGreen0.7-F145M partially in the green-on state
ComponentsrsGreen0.7-F145M
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 / molecular replacement / Resolution: 1.3 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 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 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: rsGreen0.7-F145M


Theoretical massNumber of molelcules
Total (without water)30,6531
Polymers30,6531
Non-polymers00
Water7,170398
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 area10270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.814, 61.303, 105.214
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 rsGreen0.7-F145M


Mass: 30653.459 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 38.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 200 mM NH4HCO2 20 % PEG 4000

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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: Jul 19, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→39.922 Å / Num. obs: 51172 / % possible obs: 99.2 % / Redundancy: 3.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.051 / Rrim(I) all: 0.1 / Net I/σ(I): 9.1
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
1.3-1.323.50.394951927120.830.2410.464399.4
6.88-39.923.40.05513694020.9950.0340.0651796.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.88 Å40.05 Å
Translation4.88 Å40.05 Å

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Processing

Software
NameVersionClassification
PHENIX1.15refinement
XDSdata reduction
Aimless0.6.2data scaling
PHASER2.7.16phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XOW

4xow


Resolution: 1.3→39.92 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1645 2555 5 %
Rwork0.1278 48554 -
obs0.1296 51109 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.12 Å2 / Biso mean: 13.961 Å2 / Biso min: 1.07 Å2
Refinement stepCycle: final / Resolution: 1.3→39.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1807 0 0 398 2205
Biso mean---26.97 -
Num. residues----228
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3-1.3250.20611530.1715267699
1.325-1.35210.25041320.1879263699
1.3521-1.38150.23511370.1789267999
1.3815-1.41360.21081310.162259398
1.4136-1.4490.20521530.15152694100
1.449-1.48810.17731450.13762637100
1.4881-1.53190.17321350.129271799
1.5319-1.58140.17651420.12772673100
1.5814-1.63790.14421360.1229267599
1.6379-1.70350.17461460.1231268899
1.7035-1.7810.16571390.1213268699
1.781-1.87490.14531450.1193269199
1.8749-1.99240.14581380.1105270299
1.9924-2.14620.15151340.1107269099
2.1462-2.36220.13891450.1149271699
2.3622-2.70390.14451310.1232276499
2.7039-3.40630.16651540.1239275799
3.4063-39.920.1611590.1303288098

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