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

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Basic information

Entry
Database: PDB / ID: 2okw
TitleA non-invasive GFP-based biosensor for mercury ions
ComponentsGreen fluorescent protein
KeywordsLUMINESCENT PROTEIN / mercury / biosensor
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: 1.9 Å
AuthorsChapleau, R.R. / Blomberg, R. / Ford, P.C. / Sagermann, M.
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 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
C: Green fluorescent protein
D: Green fluorescent protein
E: Green fluorescent protein
F: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)161,3906
Polymers161,3906
Non-polymers00
Water20,8611158
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
3
C: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,8981
Polymers26,8981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,8981
Polymers26,8981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,8981
Polymers26,8981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: 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)88.178, 128.843, 147.889
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: 26898.365 Da / Num. of mol.: 6 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 1158 / Source method: isolated from a natural source / Formula: H2O
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

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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: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM Pipes, 30% PEG 8000, 200mM Na-acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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 4 / Detector: CCD / Date: Jun 3, 2006 / Details: single SI crystal flat mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979454 Å / Relative weight: 1
ReflectionResolution: 1.9→19.83 Å / Num. all: 156061 / Num. obs: 155659 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.16 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 15.7

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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: 1.9→19.83 Å / 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. These residues were therefore omitted in the final model
RfactorNum. reflection% reflectionSelection details
Rfree0.2679 10643 -RANDOM
Rwork0.2323 ---
all-156061 --
obs-132734 99.7 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.576 Å20 Å20 Å2
2--1.067 Å20 Å2
3---0.509 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10632 0 0 1158 11790
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.374
X-RAY DIFFRACTIONc_bond_d0.0054

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