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- PDB-6fll: SPECTROSCOPIC AND STRUCTURAL STUDY OF QW, A EGFP MUTANT SHOWING P... -

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Basic information

Entry
Database: PDB / ID: 6fll
TitleSPECTROSCOPIC AND STRUCTURAL STUDY OF QW, A EGFP MUTANT SHOWING PHOTOSWITCHING PROPERTIES
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / GFP / EGFP / LUMINESCENCE / FLUORESCENT / PROTEIN / BIOLUMINESCENCE / PHOTOACTIVE / 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: 1.79 Å
AuthorsGarau, G. / Margheritis, E.
Funding support Italy, 1items
OrganizationGrant numberCountry
Ministero degli Affari Esteri e della Cooperazione InternazionaleSB2D-CNI-BGU Italy
Citation
Journal: Acs Chem.Biol. / Year: 2018
Title: Role of Gln222 in Photoswitching of Aequorea Fluorescent Proteins: A Twisting and H-Bonding Affair?
Authors: Storti, B. / Margheritis, E. / Abbandonato, G. / Domenichini, G. / Dreier, J. / Testa, I. / Garau, G. / Nifosi, R. / Bizzarri, R.
#1: Journal: To Be Published
Title: STRUCTURE OF THE GREEN FLUORESCENCE PROTEIN WQ
Authors: Garau, G. / Margheritis, E.
History
DepositionJan 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Feb 10, 2021Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jan 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)28,5541
Polymers28,5541
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.450, 62.710, 66.130
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: 28554.172 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 3350, 0.1 M AMMONIUM ACETATE, 0.2 M NH4F, PH 5.0
PH range: 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.96 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 10, 2017
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.79→66.13 Å / Num. obs: 20947 / % possible obs: 100 % / Redundancy: 6 % / Rmerge(I) obs: 0.183 / Rsym value: 0.12 / Net I/σ(I): 7.4
Reflection shellResolution: 1.79→1.82 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 1.4 / Rsym value: 0.761 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O24

2o24


Resolution: 1.79→45.5 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.555 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23216 1085 5.2 %RANDOM
Rwork0.20207 ---
obs0.20371 19807 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.796 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å2-0 Å2
2--0.28 Å20 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.79→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1795 0 0 123 1918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191850
X-RAY DIFFRACTIONr_bond_other_d0.0020.021683
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.9632500
X-RAY DIFFRACTIONr_angle_other_deg1.20133930
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0445223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70225.05591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32515321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.261157
X-RAY DIFFRACTIONr_chiral_restr0.0780.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212045
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02366
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0381.609893
X-RAY DIFFRACTIONr_mcbond_other0.9961.606892
X-RAY DIFFRACTIONr_mcangle_it1.7052.4051112
X-RAY DIFFRACTIONr_mcangle_other1.7042.4081113
X-RAY DIFFRACTIONr_scbond_it1.2971.746957
X-RAY DIFFRACTIONr_scbond_other1.2961.748958
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1652.5541388
X-RAY DIFFRACTIONr_long_range_B_refined3.50918.3021953
X-RAY DIFFRACTIONr_long_range_B_other3.46818.1951936
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.786→1.832 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 66 -
Rwork0.278 1439 -
obs--99.93 %

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