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- PDB-7o7u: Crystal structure of rsEGFP2 in the non-fluorescent off-state det... -

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Basic information

Entry
Database: PDB / ID: 7o7u
TitleCrystal structure of rsEGFP2 in the non-fluorescent off-state determined by serial femtosecond crystallography at room temperature
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / Reversibly 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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHadjidemetriou, K. / Woodhouse, J. / Coquelle, N. / Barends, T.R.M. / Schlichting, I. / Weik, M. / Colletier, J.-P.
CitationJournal: Chemphyschem / Year: 2022
Title: Rational Control of Off-State Heterogeneity in a Photoswitchable Fluorescent Protein Provides Switching Contrast Enhancement.
Authors: Adam, V. / Hadjidemetriou, K. / Jensen, N. / Shoeman, R.L. / Woodhouse, J. / Aquila, A. / Banneville, A.S. / Barends, T.R.M. / Bezchastnov, V. / Boutet, S. / Byrdin, M. / Cammarata, M. / ...Authors: Adam, V. / Hadjidemetriou, K. / Jensen, N. / Shoeman, R.L. / Woodhouse, J. / Aquila, A. / Banneville, A.S. / Barends, T.R.M. / Bezchastnov, V. / Boutet, S. / Byrdin, M. / Cammarata, M. / Carbajo, S. / Eleni Christou, N. / Coquelle, N. / De la Mora, E. / El Khatib, M. / Moreno Chicano, T. / Bruce Doak, R. / Fieschi, F. / Foucar, L. / Glushonkov, O. / Gorel, A. / Grunbein, M.L. / Hilpert, M. / Hunter, M. / Kloos, M. / Koglin, J.E. / Lane, T.J. / Liang, M. / Mantovanelli, A. / Nass, K. / Nass Kovacs, G. / Owada, S. / Roome, C.M. / Schiro, G. / Seaberg, M. / Stricker, M. / Thepaut, M. / Tono, K. / Ueda, K. / Uriarte, L.M. / You, D. / Zala, N. / Domratcheva, T. / Jakobs, S. / Sliwa, M. / Schlichting, I. / Colletier, J.P. / Bourgeois, D. / Weik, M.
History
DepositionApr 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 19, 2022Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_id_ISSN / _citation.journal_volume / _entity_src_gen.gene_src_common_name
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)28,5321
Polymers28,5321
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-2 kcal/mol
Surface area11200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.740, 63.090, 71.530
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: 28532.203 Da / Num. of mol.: 1
Mutation: M1_S2insV, F64L, S65T, H231L, A206K, Q69L, V163S, T65A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.05 Å3/Da / Density % sol: 39.88 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 8 / Details: 100 mM HEPES pH 8.0, 2 M ammonium sulphate

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Data collection

DiffractionMean temperature: 277.15 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.362 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Jun 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.362 Å / Relative weight: 1
ReflectionResolution: 1.7→17.21 Å / Num. obs: 27394 / % possible obs: 100 % / Redundancy: 835 % / CC star: 0.999 / R split: 0.068 / Net I/σ(I): 10
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 548 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1810 / CC star: 0.924 / R split: 0.563 / % possible all: 100
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
CrystFEL0.6.2data reduction
CrystFEL0.8.0data scaling
PHASER2.8.3phasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T39

6t39


Resolution: 1.7→17.21 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.212 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2147 1214 4.6 %RANDOM
Rwork0.1797 ---
obs0.1813 25154 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.92 Å2 / Biso mean: 21.603 Å2 / Biso min: 10.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20 Å2
2--0.43 Å20 Å2
3---0.34 Å2
Refinement stepCycle: final / Resolution: 1.7→17.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1905 0 0 177 2082
Biso mean---36.88 -
Num. residues----238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132609
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172313
X-RAY DIFFRACTIONr_angle_refined_deg1.7281.6793584
X-RAY DIFFRACTIONr_angle_other_deg1.3851.6095443
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.2745.413351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77924.046131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.82815445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.308159
X-RAY DIFFRACTIONr_chiral_restr0.0840.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023360
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02538
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 85 -
Rwork0.361 1812 -
all-1897 -
obs--100 %

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