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- PDB-2oky: A non-invasive GFP-based biosensor for mercury ions -

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Basic information

Entry
Database: PDB / ID: 2oky
TitleA non-invasive GFP-based biosensor for mercury ions
ComponentsGreen fluorescent protein
KeywordsLUMINESCENT PROTEIN / mercury sensor / 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
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSagermann, M. / Chapleau, R.R.
Citation
Journal: Protein Sci. / Year: 2008
Title: Design of a highly specific and noninvasive biosensor suitable for real-time in vivo imaging of mercury (II) uptake.
Authors: Chapleau, R.R. / Blomberg, R. / Ford, P.C. / Sagermann, M.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Local complexity of amino acid interactions in a protein core.
Authors: Jain, R.K. / Ranganathan, R.
#2: Journal: Science / Year: 1996
Title: Crystal structure of the Aequorea victoria green fluorescent protein.
Authors: Ormo, M. / Cubitt, A.B. / Kallio, K. / Gross, L.A. / Tsien, R.Y. / Remington, S.J.
History
DepositionJan 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,7972
Polymers53,7972
Non-polymers00
Water2,054114
1
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,8981
Polymers26,8981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,8981
Polymers26,8981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.240, 87.240, 119.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsIN the crystal, eGFP is a dimer of chains A, B.

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Components

#1: Protein Green fluorescent protein


Mass: 26898.365 Da / Num. of mol.: 2 / Mutation: S65T, R80Q, S205C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pet151 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAUTHORS STATE THAT RESIDUE 64 IS A LEUCINE. RESIDUE 65 HAS BEEN MUTATED FROM SER TO THR AND RESIDUE ...AUTHORS STATE THAT RESIDUE 64 IS A LEUCINE. RESIDUE 65 HAS BEEN MUTATED FROM SER TO THR AND RESIDUE 80 IS AN ARG TO GLN MUTATION. RESIDUE 80 IS LISTED AS A GLN IN THE DATABASE REFERENCE BUT IS AN ARG ACCORDING TO ROUWENDAL ET AL., 1997 PLANT MOL. BIOL. 33, 989-999 RESIDUES THR 65, TYR 66, GLY 67 CONSTITUTE THE CHROMOPHORE CRO RESIDUE

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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: 2.11 Å3/Da / Density % sol: 41.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 32% PEG 8000, 100mM PIPES, 200mM ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979454 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 6, 2006 / Details: Single SI crystal flat mirror
RadiationMonochromator: SI crystal (111) flat mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979454 Å / Relative weight: 1
ReflectionResolution: 2.4→19.936 Å / Num. all: 18687 / Num. obs: 18556 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Rmerge(I) obs: 0.036 / Rsym value: 0.055 / Net I/σ(I): 38.46
Reflection shellResolution: 2.4→2.6 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 9.99 / Num. unique all: 3838 / Rsym value: 0.33 / % possible all: 98.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EMB

1emb


Resolution: 2.4→19.9 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: First 6 residues and the last c-terminal residues could not be modeled into the density.
RfactorNum. reflection% reflectionSelection details
Rfree0.302 2047 -random
Rwork0.2251 ---
obs0.2251 18556 99.7 %-
all-18617 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.465 Å20 Å2-6.465 Å2
2--0 Å212.929 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3544 0 0 114 3658
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.824
X-RAY DIFFRACTIONc_bond_d0.0142

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