[Data set] A novel biosensor for ferrous iron developed via CoBiSe: A computational method for rapid biosensor design
Registered ARC content:
root
README.md
isa.investigation.xlsx
assays
CNA
README.md
isa.assay.xlsx
dataset
CNAs
CNA_results - 251106_30RexYFP_dimer_CNA.pse - 251106_QUE2m_CNA.pse - 251107_DtxR_CNA.pse - 251107_HyPer3_OxyRrd.pse - 251107_MalE_CNA.pse - 251107_Perceval_GlnK_trimer.pse - 251107_TreCO4_CNA.pse
Expression_and_Purification
README.md
isa.assay.xlsx
In_vitro_characterization_IronSenseR
README.md
isa.assay.xlsx
dataset
In vitro
Eva_241025_MDtxRGA_180-192_20mM_MOPS_pH7.0_0-25uM_FeIISO4.xlsx
Eva_250129_MDtxRGA_G149_pAZ198_199_200_biol.RepI-III_0-25_FeSO4.xlsx
Eva_251023_pAZ191_MDtxR_G149_Tit_CaSo4_CuSO4_ZnSO4_20mM_MOPS_pH7.0.xlsx
In_vivo_C_glutamicum
README.md
isa.assay.xlsx
dataset
20250525_IronBiosensor.xlsx
20250526_IronBiosensor_afterfridge.xlsx
20250526_IronBiosensor_afterfridge_raw.xlsx
20250526_IronBiosensor_normiert_after fridge.pzfx
In_vivo_E_coli
README.md
isa.assay.xlsx
dataset
241218_MDtxR_GA
Figure_description_iron_paper_MAN.docx
GA 20 BPD C1.tiff
GA 20 BPD C2.tiff
GA 20 BPD TD.tiff
GA 20 BPD merge.tiff
GA 20 BPD ratio ROIs.tiff
GA 20 BPD ratio.tiff
GA 250 BPD C1.tiff
GA 250 BPD C2.tiff
GA 250 BPD TD.tiff
GA 250 BPD merge.tiff
GA 250 BPD ratio ROIs.tiff
GA 250 BPD ratio.tiff
250609_MAN_IronSenseR in vivo
2025-06-08_pAZ191_198_199_200_BPD_Titrations.prism
2025-06-08_pAZ191_198_199_200_BPD_Titrations.xlsx
MDtxRGA in vivo Tecan M&M.docx
Unknown.png
250611
24h 2025-06-12 - 01_2025-06-12_MDtxR_24h_WT_phase_LUT.pdf - 02_2025-06-12_MDtxR_24h_H79A_phase_LUT.pdf - 03_2025-06-12_MDtxR_24h_H98A_phase_LUT.pdf - 04_2025-06-12_MDtxR_24h_C102A_phase_LUT.pdf
48h nur Mutanten 2025-02-26 - 2025-02-26_MDtxR_C102A_48h_Publ_1.pdf - 2025-02-26_MDtxR_C102A_48h_Publ_1_phase_LUT.pdf - 2025-02-26_MDtxR_H79A_48h_Publ_1.pdf - 2025-02-26_MDtxR_H79A_48h_Publ_1_phase_LUT.pdf - 2025-02-26_MDtxR_H98A_48h_Publ_1.pdf - 2025-02-26_MDtxR_H98A_48h_Publ_1_phase_LUT.pdf
alte 48h WT Messung-passt zu altem BoxPlot - 2024-12-18_MDtxR_WT_48h_Publ_1_besser_aber_einmalig.pdf - 2024-12-18_MDtxR_WT_48h_Publ_1_einmaligbesser_newLUT.pdf - 2024-12-18_MDtxR_WT_48h_Publ_1_newLUT.pdf - 2024-12-18_MDtxR_WT_48h_Publ_1_semigut.pdf
250620
BoxPlots - 24h - 24h_all.svg - 24h_all_oldNormalization.svg - 24h_only_triplicate.svg - 24h_only_triplicate_oldNormalization.svg - 48h - 48h_all.svg - 48h_all_oldNormalization.svg - 48h_only_triplicates.svg - 48h_only_triplicates_oldNormalization.svg
Microscopy Images - 24h - C102A - 2025-06-12_MDtxR_24h_C102A_phase_06.pdf - 2025-06-12_MDtxR_24h_C102A_phase_08.pdf - 2025-06-12_MDtxR_24h_C102A_physics_06.pdf - 2025-06-12_MDtxR_24h_C102A_physics_06_2.pdf - 2025-06-12_MDtxR_24h_C102A_physics_08.pdf - H79A - 2025-06-12_MDtxR_24h_H79A_phase_06.pdf - 2025-06-12_MDtxR_24h_H79A_phase_08.pdf - 2025-06-12_MDtxR_24h_H79A_physics_06.pdf - 2025-06-12_MDtxR_24h_H79A_physics_06_2.pdf - 2025-06-12_MDtxR_24h_H79A_physics_08.pdf - H98A - 2025-06-12_MDtxR_24h_H98A_phase_06.pdf - 2025-06-12_MDtxR_24h_H98A_phase_08.pdf - 2025-06-12_MDtxR_24h_H98A_physics_06.pdf - 2025-06-12_MDtxR_24h_H98A_physics_06_2.pdf - 2025-06-12_MDtxR_24h_H98A_physics_08.pdf - WT - 2025-06-12_MDtxR_24h_WT_phase_06.pdf - 2025-06-12_MDtxR_24h_WT_phase_08.pdf - 2025-06-12_MDtxR_24h_WT_physics_06.pdf - 2025-06-12_MDtxR_24h_WT_physics_06_2.pdf - 2025-06-12_MDtxR_24h_WT_physics_08.pdf - 48h - C102A - 2025-02-26_MDtxR_48h_C102A_phase_06.pdf - 2025-02-26_MDtxR_48h_C102A_phase_08.pdf - 2025-02-26_MDtxR_48h_C102A_physics06.pdf - 2025-02-26_MDtxR_48h_C102A_physics_08.pdf - H79A - 2025-02-26_MDtxR_48h_H79A_phase_06.pdf - 2025-02-26_MDtxR_48h_H79A_phase_08.pdf - 2025-02-26_MDtxR_48h_H79A_physics_06.pdf - 2025-02-26_MDtxR_48h_H79A_physics_08.pdf - H98A - 2025-02-26_MDtxR_48h_H98A_phase_06.pdf - 2025-02-26_MDtxR_48h_H98A_phase_08.pdf - 2025-02-26_MDtxR_48h_H98A_physics_06.pdf - 2025-02-26_MDtxR_48h_H98A_physics_08.pdf - WT - 2025-02-26_MDtxR_48h_WT_phase_06.pdf - 2025-02-26_MDtxR_48h_WT_phase_08.pdf - 2025-02-26_MDtxR_48h_WT_physics_06.pdf - 2025-02-26_MDtxR_48h_WT_physics_08.pdf
Tecan - 2025-06-08_pAZ191_198_199_200_BPD_Titrations.xlsx - MDtxR_invivo_BPD_Titration.png
In_vivo_P_putida
README.md
isa.assay.xlsx
dataset
250508
2025_05_07.prism
2025_05_07.xlsx
2025_05_07_Pputida_Data.prism
2025_05_07_Pputida_Data.xlsx
Extern BioSensor in P putida.pdf
Unknown-1.png
Unknown.png
image001.png
image003.png
250527
250527_IronSenseR.xlsx
Layout 1.tif
Layout 2.tif
Project1.prism
Small_angle_Xray_scattering
README.md
isa.assay.xlsx
dataset
241115_SEC SAXS pAZ191 MDtxRGA G149
211115 SEC SAXS pAZ191 MDtxRGA G149.docx
Bildschirmfoto 2024-11-22 um 16.55.05.png
Structural_modeling_for_CoBiSe
README.md
isa.assay.xlsx
dataset
MDtxRGA
0_241017_af3_mdtxrga_i138 - fold_241017_af3_mdtxrga_i138_full_data.pse
10_241017_af3_mdtxrga_s148 - fold_241017_af3_mdtxrga_s148_full_data.pse
11_241017_af3_mdtxrga_g149 - fold_241017_af3_mdtxrga_g149_full_data.pse
12_241017_af3_mdtxrga_v150 - fold_241017_af3_mdtxrga_v150_full_data.pse
1_241017_af3_mdtxrga_g139 - fold_241017_af3_mdtxrga_g139_full_data.pse
2_241017_af3_mdtxrga_l140 - fold_241017_af3_mdtxrga_l140_full_data.pse
3_241017_af3_mdtxrga_d141 - fold_241017_af3_mdtxrga_d141_full_data.pse
4_241017_af3_mdtxrga_q142 - fold_241017_af3_mdtxrga_q142_full_data.pse
5_241017_af3_mdtxrga_a143 - fold_241017_af3_mdtxrga_a143_full_data.pse
6_241017_af3_mdtxrga_d144 - fold_241017_af3_mdtxrga_d144_full_data.pse
7_241017_af3_mdtxrga_e145 - fold_241017_af3_mdtxrga_e145_full_data.pse
8_241017_af3_mdtxrga_p146 - fold_241017_af3_mdtxrga_p146_full_data.pse
9_241017_af3_mdtxrga_d147 - fold_241017_af3_mdtxrga_d147_full_data.pse
Structural_modeling_of_sFP_Biosensors
README.md
isa.assay.xlsx
dataset
Structural data sFP biosensors
AF3 - fold_240114_af3_atpque7mu - fold_240114_af3_atpque7mu.pdf - fold_240114_af3_atpque7mu.zip - fold_240114_af3_atpque7mu_full_data_0.json - fold_240114_af3_atpque7mu_full_data_1.json - fold_240114_af3_atpque7mu_full_data_2.json - fold_240114_af3_atpque7mu_full_data_3.json - fold_240114_af3_atpque7mu_full_data_4.json - fold_240114_af3_atpque7mu_job_request.json - fold_240114_af3_atpque7mu_model_0.cif - fold_240114_af3_atpque7mu_model_1.cif - fold_240114_af3_atpque7mu_model_2.cif - fold_240114_af3_atpque7mu_model_3.cif - fold_240114_af3_atpque7mu_model_4.cif - fold_240114_af3_atpque7mu_summary_confidences_0.json - fold_240114_af3_atpque7mu_summary_confidences_1.json - fold_240114_af3_atpque7mu_summary_confidences_2.json - fold_240114_af3_atpque7mu_summary_confidences_3.json - fold_240114_af3_atpque7mu_summary_confidences_4.json - fold_240524_af3_malb2 - fold_240524_af3_malb2.pdf - fold_240524_af3_malb2.zip - fold_240524_af3_malb2_full_data_0.json - fold_240524_af3_malb2_full_data_1.json - fold_240524_af3_malb2_full_data_2.json - fold_240524_af3_malb2_full_data_3.json - fold_240524_af3_malb2_full_data_4.json - fold_240524_af3_malb2_job_request.json - fold_240524_af3_malb2_model_0.cif - fold_240524_af3_malb2_model_1.cif - fold_240524_af3_malb2_model_2.cif - fold_240524_af3_malb2_model_3.cif - fold_240524_af3_malb2_model_4.cif - fold_240524_af3_malb2_summary_confidences_0.json - fold_240524_af3_malb2_summary_confidences_1.json - fold_240524_af3_malb2_summary_confidences_2.json - fold_240524_af3_malb2_summary_confidences_3.json - fold_240524_af3_malb2_summary_confidences_4.json - pIDDT_fold_240524_af3_malb2_model_all.pse - fold_240524_af3_tre_co4 - fold_240524_af3_tre_co4.pdf - fold_240524_af3_tre_co4.zip - fold_240524_af3_tre_co4_full_data_0.json - fold_240524_af3_tre_co4_full_data_1.json - fold_240524_af3_tre_co4_full_data_2.json - fold_240524_af3_tre_co4_full_data_3.json - fold_240524_af3_tre_co4_full_data_4.json - fold_240524_af3_tre_co4_job_request.json - fold_240524_af3_tre_co4_model_0.cif - fold_240524_af3_tre_co4_model_1.cif - fold_240524_af3_tre_co4_model_2.cif - fold_240524_af3_tre_co4_model_3.cif - fold_240524_af3_tre_co4_model_4.cif - fold_240524_af3_tre_co4_summary_confidences_0.json - fold_240524_af3_tre_co4_summary_confidences_1.json - fold_240524_af3_tre_co4_summary_confidences_2.json - fold_240524_af3_tre_co4_summary_confidences_3.json - fold_240524_af3_tre_co4_summary_confidences_4.json - pIDDT_fold_240524_af3_tre_co4_model_all.pse - fold_250114_af3_atpque2m - fold_250114_af3_atpque2m.pdf - fold_250114_af3_atpque2m.zip - fold_250114_af3_atpque2m_full_data_0.json - fold_250114_af3_atpque2m_full_data_1.json - fold_250114_af3_atpque2m_full_data_2.json - fold_250114_af3_atpque2m_full_data_3.json - fold_250114_af3_atpque2m_full_data_4.json - fold_250114_af3_atpque2m_job_request.json - fold_250114_af3_atpque2m_model_0.cif - fold_250114_af3_atpque2m_model_1.cif - fold_250114_af3_atpque2m_model_2.cif - fold_250114_af3_atpque2m_model_3.cif - fold_250114_af3_atpque2m_model_4.cif - fold_250114_af3_atpque2m_summary_confidences_1.json - fold_250114_af3_atpque2m_summary_confidences_2.json - fold_250114_af3_atpque2m_summary_confidences_3.json - fold_250114_af3_atpque2m_summary_confidences_4.json - fold_250114_af3_atpque2mfold_250114_af3_atpque2m_summary_confidences_0.json - pIDDT_fold_250114_af3_atpque2m_model_0.png - pIDDT_fold_250114_af3_atpque2m_model_all.pse - fold_250114_af3_hyper3 - fold_250114_af3_hyper3.pdf - fold_250114_af3_hyper3.zip - fold_250114_af3_hyper3_full_data_0.json - fold_250114_af3_hyper3_full_data_1.json - fold_250114_af3_hyper3_full_data_2.json - fold_250114_af3_hyper3_full_data_3.json - fold_250114_af3_hyper3_full_data_4.json - fold_250114_af3_hyper3_job_request.json - fold_250114_af3_hyper3_model_0.cif - fold_250114_af3_hyper3_model_1.cif - fold_250114_af3_hyper3_model_2.cif - fold_250114_af3_hyper3_model_3.cif - fold_250114_af3_hyper3_model_4.cif - fold_250114_af3_hyper3_summary_confidences_0.json - fold_250114_af3_hyper3_summary_confidences_1.json - fold_250114_af3_hyper3_summary_confidences_2.json - fold_250114_af3_hyper3_summary_confidences_3.json - fold_250114_af3_hyper3_summary_confidences_4.json - pIDDT_fold_250114_af3_hyper3_model_all.pse - fold_250114_af3_percevalhr - fold_250114_af3_percevalhr.pdf - fold_250114_af3_percevalhr.zip - fold_250114_af3_percevalhr_full_data_0.json - fold_250114_af3_percevalhr_full_data_1.json - fold_250114_af3_percevalhr_full_data_2.json - fold_250114_af3_percevalhr_full_data_3.json - fold_250114_af3_percevalhr_full_data_4.json - fold_250114_af3_percevalhr_job_request.json - fold_250114_af3_percevalhr_model_0.cif - fold_250114_af3_percevalhr_model_1.cif - fold_250114_af3_percevalhr_model_2.cif - fold_250114_af3_percevalhr_model_3.cif - fold_250114_af3_percevalhr_model_4.cif - fold_250114_af3_percevalhr_summary_confidences_0.json - fold_250114_af3_percevalhr_summary_confidences_1.json - fold_250114_af3_percevalhr_summary_confidences_2.json - fold_250114_af3_percevalhr_summary_confidences_3.json - fold_250114_af3_percevalhr_summary_confidences_4.json - pIDDT_fold_250114_af3_percevalhr_full_data.pse - fold_250114_af3_rexyfp - fold_250114_af3_rexyfp.pdf - fold_250114_af3_rexyfp.zip - fold_250114_af3_rexyfp_full_data_0.json - fold_250114_af3_rexyfp_full_data_1.json - fold_250114_af3_rexyfp_full_data_2.json - fold_250114_af3_rexyfp_full_data_3.json - fold_250114_af3_rexyfp_full_data_4.json - fold_250114_af3_rexyfp_job_request.json - fold_250114_af3_rexyfp_model_0.cif - fold_250114_af3_rexyfp_model_1.cif - fold_250114_af3_rexyfp_model_2.cif - fold_250114_af3_rexyfp_model_3.cif - fold_250114_af3_rexyfp_model_4.cif - fold_250114_af3_rexyfp_summary_confidences_0.json - fold_250114_af3_rexyfp_summary_confidences_1.json - fold_250114_af3_rexyfp_summary_confidences_2.json - fold_250114_af3_rexyfp_summary_confidences_3.json - fold_250114_af3_rexyfp_summary_confidences_4.json - pIDDT_fold_250114_af3_rexyfp_model_all.pse
studies
CoBiSe
README.md
isa.study.xlsx
resources
DtxR
DtxR_C_glutamicum.pdb
FASTA
sFP biosensors - fold_240114_af3_atpque7mu_model_0_A.prot - fold_240524_af3_malb2_model_0_A.prot - fold_240524_af3_tre_co4_model_0_A.prot - fold_250114_af3_atpque2m_model_0_A.prot - fold_250114_af3_hyper3_model_0_A.prot - fold_250114_af3_percevalhr_model_0_A.prot - fold_250114_af3_rexyfp_model_0_A.prot
Functional_characterization_IronSenseR
README.md
isa.study.xlsx
resources
Plasmids
pAZ180_pRSET_10xHis_EK_MDtxRGA_I138.dna
pAZ181_pRSET_10xHis_EK_MDtxRGA_G139.dna
pAZ182_pRSET_10xHis_EK_MDtxRGA_L140.dna
pAZ183_pRSET_10xHis_EK_MDtxRGA_D141.dna
pAZ184_pRSET_10xHis_EK_MDtxRGA_Q142.dna
pAZ185_pRSET_10xHis_EK_MDtxRGA_A143.dna
pAZ186_pRSET_10xHis_EK_MDtxRGA_D144.dna
pAZ187_pRSET_10xHis_EK_MDtxRGA_E145.dna
pAZ188_pRSET_10xHis_EK_MDtxRGA_P146.dna
pAZ189_pRSET_10xHis_EK_MDtxRGA_D147.dna
pAZ190_pRSET_10xHis_EK_MDtxRGA_S148.dna
pAZ191_pRSET_10xHis_EK_MDtxRGA_G149.dna
pAZ192_pRSET_10xHis_EK_MDtxRGA_V150.dna
pAZ198_pRSET_10xHis_EK_MDtxRGA_G149_H79A.dna
pAZ199_pRSET_10xHis_EK_MDtxRGA_G149_H98A.dna
pAZ200_pRSET_10xHis_EK_MDtxRGA_G149_C102A.dna
pAZ240_pRSET_10xHis_lin.dna
Strains
C glutamicum.md