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- PDB-6zui: Crystal structure of the Cys-Ser mutant of the cpYFP-based biosen... -

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Basic information

Entry
Database: PDB / ID: 6zui
TitleCrystal structure of the Cys-Ser mutant of the cpYFP-based biosensor for hypochlorous acid
ComponentsHTH-type transcriptional repressor NemR,Green fluorescent protein,Green fluorescent protein,HTH-type transcriptional repressor NemR
KeywordsFLUORESCENT PROTEIN / biosensor / hypohalous acid / cpYFP / yellow fluorescent protein
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Tetracyclin repressor-like, C-terminal domain / Tetracyclin repressor-like, C-terminal domain / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related ...Tetracyclin repressor-like, C-terminal domain / Tetracyclin repressor-like, C-terminal domain / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Homeobox-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Green fluorescent protein / HTH-type transcriptional repressor NemR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Aequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.20008218184 Å
AuthorsTossounian, M.A. / Van Molle, I. / Messens, J.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO) Belgium
Citation
Journal: Nat Commun / Year: 2022
Title: Hypocrates is a genetically encoded fluorescent biosensor for (pseudo)hypohalous acids and their derivatives.
Authors: Kostyuk, A.I. / Tossounian, M.A. / Panova, A.S. / Thauvin, M. / Raevskii, R.I. / Ezerina, D. / Wahni, K. / Van Molle, I. / Sergeeva, A.D. / Vertommen, D. / Gorokhovatsky, A.Y. / Baranov, M.S. ...Authors: Kostyuk, A.I. / Tossounian, M.A. / Panova, A.S. / Thauvin, M. / Raevskii, R.I. / Ezerina, D. / Wahni, K. / Van Molle, I. / Sergeeva, A.D. / Vertommen, D. / Gorokhovatsky, A.Y. / Baranov, M.S. / Vriz, S. / Messens, J. / Bilan, D.S. / Belousov, V.V.
#1: Journal: Biorxiv / Year: 2021
Title: Monitoring oxidative inflammatory processes in live cells and tissue with Hypocrates, a genetically encoded biosensor for hypochlorite
Authors: Kostyuk, A.I. / Tossounian, M.A. / Panova, A.S. / Thauvin, M. / Wahni, K. / Van Molle, I. / Raevskii, R.I. / Baranov, M.S. / Vriz, S. / Messens, J. / Bilan, D.S. / Belousov, V.V.
History
DepositionJul 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN
Revision 1.3Oct 16, 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: HTH-type transcriptional repressor NemR,Green fluorescent protein,Green fluorescent protein,HTH-type transcriptional repressor NemR


Theoretical massNumber of molelcules
Total (without water)49,6331
Polymers49,6331
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.232, 95.437, 106.246
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-662-

HOH

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Components

#1: Protein HTH-type transcriptional repressor NemR,Green fluorescent protein,Green fluorescent protein,HTH-type transcriptional repressor NemR / Bleach-sensing transcription factor / Redox-regulated transcription factor NemR


Mass: 49632.641 Da / Num. of mol.: 1 / Mutation: C353S
Source method: isolated from a genetically manipulated source
Details: The protein contains a chromophore (CR2 = Gly-Tyr-Gly) within the cpYFP domain.,The protein contains a chromophore (CR2 = Gly-Tyr-Gly) within the cpYFP domain.,The protein contains a ...Details: The protein contains a chromophore (CR2 = Gly-Tyr-Gly) within the cpYFP domain.,The protein contains a chromophore (CR2 = Gly-Tyr-Gly) within the cpYFP domain.,The protein contains a chromophore (CR2 = Gly-Tyr-Gly) within the cpYFP domain.,The protein contains a chromophore (CR2 = Gly-Tyr-Gly) within the cpYFP domain.
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Aequorea victoria (jellyfish)
Strain: K12 / Gene: nemR, ydhM, b1649, JW5874, GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P67430, UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris (0.1 M, pH 8), CaCl2 (0.1 M), MgCl2 (0.1 M) and PE15/4 (15%) Protein concentration:7 mg/mL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980113 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980113 Å / Relative weight: 1
ReflectionResolution: 2.09962866868→47.72 Å / Num. obs: 22368 / % possible obs: 83 % / Redundancy: 9.3 % / Biso Wilson estimate: 34.3012936225 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Net I/σ(I): 16.1
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.62 / Num. unique obs: 924 / CC1/2: 0.814

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YZE, 3O77

4yze

3o77


Resolution: 2.20008218184→47.7185 Å / SU ML: 0.329732416594 / Cross valid method: FREE R-VALUE / σ(F): 1.33787706633 / Phase error: 31.970318773
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.272940666147 1136 5.10309509905 %
Rwork0.198501182278 21125 -
obs0.202233998777 22261 94.2025305742 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.4430328993 Å2
Refinement stepCycle: LAST / Resolution: 2.20008218184→47.7185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 0 185 3497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009922046689383386
X-RAY DIFFRACTIONf_angle_d1.004436323574567
X-RAY DIFFRACTIONf_chiral_restr0.0484754324563498
X-RAY DIFFRACTIONf_plane_restr0.00446804816815594
X-RAY DIFFRACTIONf_dihedral_angle_d6.093895311882787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.30020.3906716047991270.2852762185712459X-RAY DIFFRACTION89.2955801105
2.3002-2.42150.3532036793621620.2588550026132670X-RAY DIFFRACTION97.0195272354
2.4215-2.57320.3254968747851210.234252644042708X-RAY DIFFRACTION97.0830473576
2.5732-2.77180.3035133966141680.2236230642422663X-RAY DIFFRACTION96.5552523874
2.7718-3.05070.3435651732591550.2315801458542652X-RAY DIFFRACTION95.6714383095
3.0507-3.49210.2769004848991090.2045416546382697X-RAY DIFFRACTION94.7972972973
3.4921-4.39920.2167695453361420.1662264370052643X-RAY DIFFRACTION93.6764211234
4.3992-47.71850.2336438289571520.1666264427572633X-RAY DIFFRACTION89.8097387939

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