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- PDB-5o8a: Crystal Structure of rsEGFP2 in the non-fluorescent off-state det... -

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Basic information

Entry
Database: PDB / ID: 5o8a
TitleCrystal Structure of rsEGFP2 in the non-fluorescent off-state determined by SFX
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / photoswitching on state fluorescent state chromophore SFX serial femtosecond crystallography CXI LCLS time resolved crystallography chromohore isomerisation
Function / homology
Function and homology information


regulation of viral transcription / viral transcription / bioluminescence / generation of precursor metabolites and energy / transcription antitermination / virion component / host cell cytoplasm / host cell nucleus / structural molecule activity / zinc ion binding
Similarity search - Function
Pneumovirus matrix 2-1 / Pneumovirus matrix protein 2 (M2) / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein ...Pneumovirus matrix 2-1 / Pneumovirus matrix protein 2 (M2) / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / 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
Protein M2-1 / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCoquelle, N. / Sliwa, M. / Woodhouse, J. / Schiro, G. / Adam, V. / Aquila, A. / Barends, T.R.M. / Boutet, S. / Byrdin, M. / Carbajo, S. ...Coquelle, N. / Sliwa, M. / Woodhouse, J. / Schiro, G. / Adam, V. / Aquila, A. / Barends, T.R.M. / Boutet, S. / Byrdin, M. / Carbajo, S. / De la Mora, E. / Doak, R.B. / Feliks, M. / Fieschi, F. / Foucar, L. / Guillon, V. / Hilpert, M. / Hunter, M. / Jakobs, S. / Koglin, J.E. / Kovacsova, G. / Lane, T.J. / Levy, B. / Liang, M. / Nass, K. / Ridard, J. / Robinson, J.S. / Roome, C.M. / Ruckebusch, C. / Seaberg, M. / Thepaut, M. / Cammarata, M. / Demachy, I. / Field, M. / Shoeman, R.L. / Bourgeois, D. / Colletier, J.P. / Schlichting, I. / Weik, M.
CitationJournal: Nat Chem / Year: 2018
Title: Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography.
Authors: Coquelle, N. / Sliwa, M. / Woodhouse, J. / Schiro, G. / Adam, V. / Aquila, A. / Barends, T.R.M. / Boutet, S. / Byrdin, M. / Carbajo, S. / De la Mora, E. / Doak, R.B. / Feliks, M. / Fieschi, ...Authors: Coquelle, N. / Sliwa, M. / Woodhouse, J. / Schiro, G. / Adam, V. / Aquila, A. / Barends, T.R.M. / Boutet, S. / Byrdin, M. / Carbajo, S. / De la Mora, E. / Doak, R.B. / Feliks, M. / Fieschi, F. / Foucar, L. / Guillon, V. / Hilpert, M. / Hunter, M.S. / Jakobs, S. / Koglin, J.E. / Kovacsova, G. / Lane, T.J. / Levy, B. / Liang, M. / Nass, K. / Ridard, J. / Robinson, J.S. / Roome, C.M. / Ruckebusch, C. / Seaberg, M. / Thepaut, M. / Cammarata, M. / Demachy, I. / Field, M. / Shoeman, R.L. / Bourgeois, D. / Colletier, J.P. / Schlichting, I. / Weik, M.
History
DepositionJun 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: diffrn_source / entity ...diffrn_source / entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site ..._diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.2Dec 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Nov 14, 2018Group: Data collection / Category: diffrn / Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.4Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.5Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Jan 17, 2024Group: Refinement description / Category: 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)28,1001
Polymers28,1001
Non-polymers00
Water5,603311
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-3 kcal/mol
Surface area11870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.530, 62.850, 71.760
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
Details: HIS A -8 EXPRESSION TAG HIS A -7 EXPRESSION TAG HIS A -6 EXPRESSION TAG HIS A -5 EXPRESSION TAG HIS A -4 EXPRESSION TAG HIS A -3 EXPRESSION TAG THR A -2 EXPRESSION TAG ASP A -1 EXPRESSION ...Details: HIS A -8 EXPRESSION TAG HIS A -7 EXPRESSION TAG HIS A -6 EXPRESSION TAG HIS A -5 EXPRESSION TAG HIS A -4 EXPRESSION TAG HIS A -3 EXPRESSION TAG THR A -2 EXPRESSION TAG ASP A -1 EXPRESSION TAG PRO A 0 EXPRESSION TAG MET A 1 EXPRESSION TAG VAL A 2 MET 1 ENGINEERED MUTATION LEU A 65 PHE 64 ENGINEERED MUTATION PIA A 68 SER 65 CHROMOPHORE PIA A 68 TYR 66 CHROMOPHORE PIA A 68 GLY 67 CHROMOPHORE LEU A 70 GLN 69 ENGINEERED MUTATION SER A 164 VAL 163 ENGINEERED MUTATION LYS A 207 ALA 206 ENGINEERED MUTATION LEU A 232 HIS 231 ENGINEERED MUTATION
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212, UniProt: A0A1S5SHT2*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O

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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: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 8 / Details: 2 M ammonium sulphate, 20 mM NaCl, 120 mM HEPES

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.3 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: May 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 1.7→47.021 Å / Num. obs: 25880 / % possible obs: 99.8 % / Redundancy: 665 % / Net I/σ(I): 11.5

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
CrystFEL0.6.1data reduction
CrystFEL0.6.1data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DTY

5dty


Resolution: 1.7→17.251 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.33
RfactorNum. reflection% reflection
Rfree0.1838 1565 5 %
Rwork0.1512 --
obs0.1529 25880 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→17.251 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 0 311 2271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074018
X-RAY DIFFRACTIONf_angle_d0.9635424
X-RAY DIFFRACTIONf_dihedral_angle_d14.0422370
X-RAY DIFFRACTIONf_chiral_restr0.062580
X-RAY DIFFRACTIONf_plane_restr0.006704

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