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- PDB-6un5: Crystal structure of green fluorescent protein (GFP); S65T, Y66(2... -

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Basic information

Entry
Database: PDB / ID: 6un5
TitleCrystal structure of green fluorescent protein (GFP); S65T, Y66(2,3,5-F3Y); ih circular permutant (50-51)
ComponentsGreen fluorescent protein,Green fluorescent protein
KeywordsFLUORESCENT PROTEIN / GFP
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 / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsLin, C.-Y. / Boxer, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)118044 United States
CitationJournal: J.Phys.Chem.B / Year: 2020
Title: Unusual Spectroscopic and Electric Field Sensitivity of Chromophores with Short Hydrogen Bonds: GFP and PYP as Model Systems.
Authors: Lin, C.Y. / Boxer, S.G.
History
DepositionOct 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
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.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 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
Revision 1.4Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein,Green fluorescent protein
B: Green fluorescent protein,Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)56,5372
Polymers56,5372
Non-polymers00
Water5,927329
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-7 kcal/mol
Surface area19350 Å2
Unit cell
Length a, b, c (Å)48.394, 68.464, 60.596
Angle α, β, γ (deg.)90.00, 102.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Green fluorescent protein,Green fluorescent protein


Mass: 28268.502 Da / Num. of mol.: 2
Mutation: A72S, Q80R, T105K, E111V, I128T, K166T, I167V, S205T, A206V, S232R, Y241I, C250S,A72S, Q80R, T105K, E111V, I128T, K166T, I167V, S205T, A206V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: gfp, GFP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A059PIQ0, UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.74 Å3/Da / Density % sol: 29.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.15 M ammonium acetate, 31% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.358→38.929 Å / Num. obs: 81547 / % possible obs: 98.2 % / Redundancy: 13.36 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 24.13
Reflection shellResolution: 1.36→1.4 Å / Redundancy: 13.23 % / Rmerge(I) obs: 1.945 / Mean I/σ(I) obs: 1.31 / Num. unique obs: 5968 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.13RC2_2986refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OFK

6ofk


Resolution: 1.36→38.93 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.45
RfactorNum. reflection% reflection
Rfree0.205 4076 5 %
Rwork0.174 --
obs0.175 81545 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.16 Å2
Refinement stepCycle: LAST / Resolution: 1.36→38.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3606 0 0 329 3935
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3582-1.37420.34541270.31432413X-RAY DIFFRACTION89
1.3742-1.3910.29191410.27342672X-RAY DIFFRACTION98
1.391-1.40860.31631380.26122651X-RAY DIFFRACTION98
1.4086-1.42710.28221410.24092678X-RAY DIFFRACTION98
1.4271-1.44670.30851410.25732678X-RAY DIFFRACTION98
1.4467-1.46730.3171400.24252649X-RAY DIFFRACTION97
1.4673-1.48920.32471360.23642594X-RAY DIFFRACTION97
1.4892-1.51250.27611390.2192637X-RAY DIFFRACTION96
1.5125-1.53730.26121380.20812620X-RAY DIFFRACTION98
1.5373-1.56380.22261430.18962717X-RAY DIFFRACTION99
1.5638-1.59230.23731400.19492664X-RAY DIFFRACTION99
1.5923-1.62290.23841420.18882702X-RAY DIFFRACTION99
1.6229-1.6560.25471410.19072679X-RAY DIFFRACTION99
1.656-1.6920.25331420.19262681X-RAY DIFFRACTION99
1.692-1.73140.25991430.18712721X-RAY DIFFRACTION99
1.7314-1.77470.21151410.1782670X-RAY DIFFRACTION99
1.7747-1.82270.22621400.182666X-RAY DIFFRACTION98
1.8227-1.87630.21651370.18182620X-RAY DIFFRACTION96
1.8763-1.93690.22111420.18122685X-RAY DIFFRACTION98
1.9369-2.00610.24381390.1752676X-RAY DIFFRACTION99
2.0061-2.08640.2151440.17062724X-RAY DIFFRACTION99
2.0864-2.18130.19471420.16812693X-RAY DIFFRACTION99
2.1813-2.29630.19111430.16582731X-RAY DIFFRACTION99
2.2963-2.44020.18831440.17052719X-RAY DIFFRACTION99
2.4402-2.62860.20451390.17662646X-RAY DIFFRACTION97
2.6286-2.8930.2011420.1762689X-RAY DIFFRACTION98
2.893-3.31140.18331420.16642711X-RAY DIFFRACTION99
3.3114-4.17130.16531440.15282726X-RAY DIFFRACTION99
4.1713-38.9290.18831450.15692757X-RAY DIFFRACTION98

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