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- PDB-6oa8: Superfolder Green Fluorescent Protein with 4-cyano-L-phenylalanin... -

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Basic information

Entry
Database: PDB / ID: 6oa8
TitleSuperfolder Green Fluorescent Protein with 4-cyano-L-phenylalanine at the chromophore (position 66)
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / Unnatural amino acid / chromophore
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 / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsPiacentini, J. / Olenginski, G.M. / Brewer, S.H. / Phillips-Piro, C.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R15GM121984 United States
National Science Foundation (NSF, United States)CHE-1053946 United States
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2021
Title: Structural and spectrophotometric investigation of two unnatural amino-acid altered chromophores in the superfolder green fluorescent protein
Authors: Olenginski, G.M. / Piacentini, J. / Harris, D.R. / Runko, N. / Papoutsis, B.M. / Alter, J.R. / Hess, K.R. / Brewer, S.H. / Phillips-Piro, C.M.
History
DepositionMar 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 14, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Category: atom_site / atom_type ...atom_site / atom_type / cell / chem_comp / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_asym / struct_conf / struct_conn / struct_conn_type / struct_mon_prot_cis / struct_ref_seq_dif / struct_sheet_range / symmetry
Item: _cell.volume / _chem_comp.formula ..._cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_entry_details.has_ligand_of_interest / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _reflns.B_iso_Wilson_estimate / _software.version / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_seq_id / _symmetry.space_group_name_Hall
Description: Model completeness
Details: Since the earlier submission we have added a number of solvent molecules, riding hydrogens atoms, and a few alternate conformations of side chains upon the suggestion of the editor of our ...Details: Since the earlier submission we have added a number of solvent molecules, riding hydrogens atoms, and a few alternate conformations of side chains upon the suggestion of the editor of our manuscript currently under review at Acta cryst D.
Provider: author / Type: Coordinate replacement
Revision 2.1Aug 11, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,95416
Polymers26,9071
Non-polymers1,04715
Water5,855325
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: sfGFP is a known monomeric protein and our mutation at the chromophore did not change that.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-129 kcal/mol
Surface area11540 Å2
Unit cell
Length a, b, c (Å)55.266, 55.266, 166.483
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
Components on special symmetry positions
IDModelComponents
11A-315-

NA

21A-420-

HOH

31A-606-

HOH

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Components

#1: Protein Green fluorescent protein /


Mass: 26907.336 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 str. K-12 substr. DH10B (bacteria)
References: UniProt: A0A059PIQ0, UniProt: P42212*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsR30/S72/R80/V206 sequence differences are due to the super folder GFP sequence

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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: 2.36 Å3/Da / Density % sol: 47.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris-HCl, 2.0 M ammonium sulfate, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.37→165.76 Å / Num. obs: 55127 / % possible obs: 99.6 % / Redundancy: 13.4 % / Biso Wilson estimate: 14.45 Å2 / CC1/2: 0.999 / Net I/σ(I): 20.7
Reflection shellResolution: 1.37→1.39 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2740 / CC1/2: 0.393 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 1.37→52.45 Å / SU ML: 0.1558 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.8223
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1885 2739 4.98 %
Rwork0.1613 52237 -
obs0.1627 54976 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.7 Å2
Refinement stepCycle: LAST / Resolution: 1.37→52.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1865 0 56 325 2246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01032165
X-RAY DIFFRACTIONf_angle_d1.12992960
X-RAY DIFFRACTIONf_chiral_restr0.0872314
X-RAY DIFFRACTIONf_plane_restr0.0107391
X-RAY DIFFRACTIONf_dihedral_angle_d15.1242800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.390.3461250.31962400X-RAY DIFFRACTION92.97
1.39-1.420.32121360.27092577X-RAY DIFFRACTION98.87
1.42-1.450.2571320.24922529X-RAY DIFFRACTION99.03
1.45-1.480.28221330.23242553X-RAY DIFFRACTION99.15
1.48-1.510.22681360.21812572X-RAY DIFFRACTION99.34
1.51-1.540.21361340.22072564X-RAY DIFFRACTION99.26
1.54-1.580.24931360.20252577X-RAY DIFFRACTION99.52
1.58-1.620.23121350.17792594X-RAY DIFFRACTION99.53
1.62-1.670.23111370.1822584X-RAY DIFFRACTION99.6
1.67-1.730.18181340.17392576X-RAY DIFFRACTION99.74
1.73-1.790.17251380.16392616X-RAY DIFFRACTION99.75
1.79-1.860.17621330.16142597X-RAY DIFFRACTION99.85
1.86-1.940.19521360.15592610X-RAY DIFFRACTION99.96
1.94-2.050.19371450.15122624X-RAY DIFFRACTION99.96
2.05-2.170.17431550.14012608X-RAY DIFFRACTION100
2.17-2.340.15051350.1462646X-RAY DIFFRACTION100
2.34-2.580.1761320.14392665X-RAY DIFFRACTION100
2.58-2.950.17431340.15352699X-RAY DIFFRACTION100
2.95-3.720.16281490.1372734X-RAY DIFFRACTION99.93
3.72-52.450.18451440.15162912X-RAY DIFFRACTION99.84

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