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- PDB-7a7u: rsGreen1 in the green-on state -

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Basic information

Entry
Database: PDB / ID: 7a7u
TitlersGreen1 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 / molecular replacement / Resolution: 2.15 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 1.2Jan 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)30,7071
Polymers30,7071
Non-polymers00
Water3,135174
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 area9960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.243, 73.243, 114.734
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-436-

HOH

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Components

#1: Protein Green fluorescent protein


Mass: 30707.420 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.: 174 / 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: 3.03 Å3/Da / Density % sol: 59.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.0 M (NH4)2SO4 200 mM NaCl 100 mM Na-cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 28, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.15→47.204 Å / Num. obs: 17685 / % possible obs: 100 % / Redundancy: 25.1 % / Biso Wilson estimate: 40.85 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.012 / Rrim(I) all: 0.06 / Net I/σ(I): 36.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.15-2.2226.40.58114990.9840.1150.59399.9
8.86-47.218.40.03131910.0070.03199.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.37 Å47.2 Å
Translation5.37 Å47.2 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.6.2data scaling
PHASER2.7.16phasing
PHENIX1.11refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XOW

4xow


Resolution: 2.15→47.204 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.38
RfactorNum. reflection% reflection
Rfree0.2012 890 5.05 %
Rwork0.1595 --
obs0.1616 17619 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.91 Å2 / Biso mean: 44.8864 Å2 / Biso min: 26.04 Å2
Refinement stepCycle: final / Resolution: 2.15→47.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1774 0 0 174 1948
Biso mean---52.61 -
Num. residues----224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071901
X-RAY DIFFRACTIONf_angle_d0.9252586
X-RAY DIFFRACTIONf_chiral_restr0.061277
X-RAY DIFFRACTIONf_plane_restr0.006346
X-RAY DIFFRACTIONf_dihedral_angle_d11.7341522
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.15-2.28470.22841360.16427302866
2.2847-2.46110.24531450.172627232868
2.4611-2.70880.24471350.171927562891
2.7088-3.10060.2411450.178927702915
3.1006-3.90620.18661670.154427872954
3.9062-47.21560.18011620.150329633125

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