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- PDB-6l26: Neutron crystal structure of the mutant green fluorescent protein... -

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Basic information

Entry
Database: PDB / ID: 6l26
TitleNeutron crystal structure of the mutant green fluorescent protein (EGFP)
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / GFP / mutant / recombinant
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / trideuteriooxidanium / DEUTERATED WATER / Green fluorescent protein
Function and homology information
Biological speciesNicotiana benthamiana (plant)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / FOURIER SYNTHESIS / Resolution: 1.444 Å
AuthorsAdachi, M. / Shimizu, R. / Shibazaki, C. / Kagotani, Y. / Ostermann, A. / Schrader, T.E.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP16KT0063 Japan
CitationJournal: J Phys Chem Lett / Year: 2020
Title: Direct Observation of the Protonation States in the Mutant Green Fluorescent Protein.
Authors: Shibazaki, C. / Shimizu, R. / Kagotani, Y. / Ostermann, A. / Schrader, T.E. / Adachi, M.
History
DepositionOct 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 2.0Jun 9, 2021Group: Non-polymer description / Category: chem_comp / Item: _chem_comp.formula
Revision 2.1Nov 22, 2023Group: 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: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8652
Polymers25,8431
Non-polymers221
Water6,702372
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.857, 62.160, 69.202
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 Green fluorescent protein /


Mass: 25843.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The amino acids of TYG are processed to chromophore as CRO by post-translational reaction.
Source: (gene. exp.) Nicotiana benthamiana (plant) / Gene: gfp / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W6KDG8
#2: Chemical ChemComp-D3O / trideuteriooxidanium / perdeuterated oxonium


Mass: 22.042 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: D3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: D2O
Has ligand of interestY
Sequence detailsResidue SER 66 has been mutated to THR 66. Residues THR 66, TYR 67 and GLY 68 constitute the ...Residue SER 66 has been mutated to THR 66. Residues THR 66, TYR 67 and GLY 68 constitute the chromophore CRO 66.

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES-NaOD (pD 7.0), 5.0 % w/v PEG 2000 and 50 mM NDSB

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: NUCLEAR REACTOR / Site: FRM II / Beamline: BIODIFF / Wavelength: 2.668 Å
DetectorType: BIODIFF / Detector: IMAGE PLATE / Date: Nov 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron
Radiation wavelengthWavelength: 2.668 Å / Relative weight: 1
ReflectionResolution: 1.45→24.8 Å / Num. obs: 90310 / % possible obs: 88.9 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 7.9
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 25594 / % possible all: 73.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2WUR

2wur


Resolution: 1.444→24.764 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 15.37
RfactorNum. reflection% reflection
Rfree0.2065 1777 5 %
Rwork0.1676 --
obs0.1696 35540 88.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: final / Resolution: 0.88→39.362 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1811 0 4 1132 2947
Biso mean--22.72 27.68 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0124709
NEUTRON DIFFRACTIONf_angle_d1.3897567
NEUTRON DIFFRACTIONf_chiral_restr0.094281
NEUTRON DIFFRACTIONf_plane_restr0.008784
NEUTRON DIFFRACTIONf_dihedral_angle_d16.8341087
LS refinement shell

Refine-ID: NEUTRON DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4442-1.48330.26791070.2211203670
1.4833-1.52690.24121220.1913231681
1.5269-1.57620.2261280.179242784
1.5762-1.63250.22011340.1708255188
1.6325-1.69780.20421360.1545258190
1.6978-1.77510.20681400.1521264691
1.7751-1.86870.211410.154268192
1.8687-1.98570.19781430.1483270793
1.9857-2.13890.19051400.1618267392
2.1389-2.3540.20111370.1688259589
2.354-2.69430.22481410.181267990
2.6943-3.39310.19481500.1682286396
3.3931-24.7640.17561580.1684300896

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