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- PDB-5dtx: Crystal structure of rsEGFP2 in the fluorescent on-state -

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Basic information

Entry
Database: PDB / ID: 5dtx
TitleCrystal structure of rsEGFP2 in the fluorescent on-state
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / GFP / reversibly switchable / cis chromophore
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsAdam, V. / Martins, A.
CitationJournal: Sci Rep / Year: 2016
Title: Rational design of ultrastable and reversibly photoswitchable fluorescent proteins for super-resolution imaging of the bacterial periplasm.
Authors: El Khatib, M. / Martins, A. / Bourgeois, D. / Colletier, J.P. / Adam, V.
History
DepositionSep 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)28,1001
Polymers28,1001
Non-polymers00
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-1 kcal/mol
Surface area11770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.990, 62.910, 70.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Green fluorescent protein


Mass: 28099.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pQE-31 / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.1 / Details: 0.1 M HEPES, 1.7 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 9, 2014
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.45→47.04 Å / Num. obs: 40827 / % possible obs: 99.35 % / Redundancy: 4.3 % / Rsym value: 0.052 / Net I/σ(I): 16.1
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.3 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 1.45→47.039 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2061 2040 5 %
Rwork0.1743 --
obs0.1759 40814 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→47.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1980 0 0 343 2323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142080
X-RAY DIFFRACTIONf_angle_d1.6532819
X-RAY DIFFRACTIONf_dihedral_angle_d12.931778
X-RAY DIFFRACTIONf_chiral_restr0.077301
X-RAY DIFFRACTIONf_plane_restr0.009368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48380.29831330.24512531X-RAY DIFFRACTION100
1.4838-1.52090.23531350.21742553X-RAY DIFFRACTION100
1.5209-1.5620.23871360.18842595X-RAY DIFFRACTION100
1.562-1.6080.21971340.18352547X-RAY DIFFRACTION100
1.608-1.65990.23851360.17552572X-RAY DIFFRACTION100
1.6599-1.71920.18981360.17642578X-RAY DIFFRACTION100
1.7192-1.7880.25851350.17512576X-RAY DIFFRACTION100
1.788-1.86940.20231350.1752566X-RAY DIFFRACTION100
1.8694-1.9680.28391340.22642529X-RAY DIFFRACTION97
1.968-2.09130.18291350.16242580X-RAY DIFFRACTION99
2.0913-2.25270.21891340.18642555X-RAY DIFFRACTION98
2.2527-2.47940.21671330.18342547X-RAY DIFFRACTION98
2.4794-2.83810.2111400.17422654X-RAY DIFFRACTION100
2.8381-3.57560.19251380.15462630X-RAY DIFFRACTION99
3.5756-47.06370.16631460.1542761X-RAY DIFFRACTION99

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