cytochrome bd-II type oxidase with bound aurachin D

2026-09-02 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond em_3d_fitting_list entity entity_name_com entity_src_gen pdbx_initial_refinement_model struct_ref struct_ref_seq _em_3d_fitting_list.accession_code _em_3d_fitting_list.initial_refinement_model_id _em_3d_fitting_list.source_name _em_3d_fitting_list.type _entity.pdbx_description _entity.pdbx_ec _entity_name_com.name _entity_src_gen.pdbx_gene_src_gene _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref_seq.pdbx_db_accession REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond em_admin pdbx_entry_details pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order pdbx_validate_chiral _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.value_order _em_admin.last_update _pdbx_entry_details.has_protein_modification PDBe PDBe 2021-06-08 2021-11-17 2021-11-17 2026-09-02 German Research Foundation (DFG) 278002225/RTG 2202 Germany cytochrome bd-II type oxidase with bound aurachin D Grauel A Kaegi J terminal oxidase, Q-loop, inhibitor binding, MEMBRANE PROTEIN Grauel A Kagi J Rasmussen T Makarchuk I Oppermann S Moumbock AFA Wohlwend D Muller R Melin F Gunther S Hellwig P Bottcher B Friedrich T Structure of Escherichia coli cytochrome bd-II type oxidase with bound aurachin D. Nat Commun UK 12 6498 6498 2021 34764272 doi:10.1038/s41467-021-26835-2 2041-1723 7ose FULLOVERLAP EMDB EMD-13048 associated EM volume

Cytochrome bd-II ubiquinol oxidase Cytochrome bd-II ubiquinol oxidase 0 1 2 3

dimer of heterotrimers solubilised in amphipol A8-35 in complex with the inhibitor Aurachin D

Escherichia coli BW25113 0.208 Cytochrome bd-II ubiquinol oxidase subunit 1 Escherichia coli BW25113 0.057962468999999996 2 Escherichia coli BL21(DE3) LEVO MWDVIDLSRWQFALTALYHFLFVPLTLGLIFLLAIMETIYVVTGKTIYRDMTRFWGKLFGINFALGVATGLTMEFQFGTN WSFYSNYVGDIFGAPLAMEALMAFFLESTFVGLFFFGWQRLNKYQHLLVTWLVAFGSNLSALWILNANGWMQYPTGAHFD IDTLRMEMTSFSELVFNPVSQVKFVHTVMAGYVTGAMFIMAISAWYLLRGRERNVALRSFAIGSVFGTLAIIGTLQLGDS SAYEVAQVQPVKLAAMEGEWQTEPAPAPFHVVAWPEQDQERNAFALKIPALLGILATHSLDKPVPGLKNLMAETYPRLQR GRMAWLLMQEISQGNREPHVLQAFRGLEGDLGYGMLLSRYAPDMNHVTAAQYQAAMRGAIPQVAPVFWSFRIMVGCGSLL LLVMLIALVQTLRGKIDQHRWVLKMALWSLPLPWIAIEAGWFMTEFGRQPWAIQDILPTYSAHSALTTGQLAFSLIMIVG LYTLFLIAEVYLMQKYARLGPSAMQSEQPTQQQG P26459 7.1.1.3 Cytochrome bd-II ubiquinol oxidase subunit 2 Escherichia coli BW25113 0.042448543 2 Escherichia coli BL21(DE3) LEVO MFDYETLRFIWWLLIGVILVVFMISDGFDMGIGCLLPLVARNDDERRIVINSVGAHWEGNQVWLILAGGALFAAWPRVYA AAFSGFYVAMILVLCSLFFRPLAFDYRGKIADARWRKMWDAGLVIGSLVPPVVFGIAFGNLLLGVPFAFTPQLRVEYLGS FWQLLTPFPLLCGLLSLGMVILQGGVWLQLKTVGVIHLRSQLATKRAALLVMLCFLLAGYWLWVGIDGFVLLAQDANGPS NPLMKLVAVLPGAWMNNFVESPVLWIFPLLGFFCPLLTVMAIYRGRPGWGFLMASLMQFGVIFTAGITLFPFVMPSSVSP ISSLTLWDSTSSQLTLSIMLVIVLIFLPIVLLYTLWSYYKMWGRMTTETLRRNENELY P26458 7.1.1.3 Putative cytochrome bd-II ubiquinol oxidase subunit AppX Escherichia coli BW25113 K12 0.0035994630000000002 2 Escherichia coli BL21(DE3) LEVO MWYLLWFVGILLMCSLSTLVLVWLDPRLKS P24244 HEME B/C 0.0006185030000000001 4 HEB CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE 0.0006324869999999999 2 HDD Aurachin D 0.00036353599999999997 2 0NI Ubiquinone-8 0.000727109 2 UQ8 water 1.8015e-05 2 HOH singleParticle particle 5.6 7.0 20.0 C7H15NO4S MOPS 20.0 NaCl sodium chloride 160.0 C25H33NO Aurachin D Quantifoil R1.2/1.3 COPPER 400 CARBON HOLEY ARRAY GLOW DISCHARGE 150 AIR ETHANE 100 277 FEI VITROBOT MARK IV

45 sec incubation, 6.5 sec blotting.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 1.4000000000000001 2.4 75000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON III (4k x 4k) COUNTING 1 1836 75.0 79.0 1 800000 CTFFIND 4.1 PHASE FLIPPING AND AMPLITUDE CORRECTION C2 FOURIER SPACE 3.0 FSC 0.143 CUT-OFF RELION 3.1 125497 MAXIMUM LIKELIHOOD RELION 3.1 MAXIMUM LIKELIHOOD RELION 3.1 RELION 3.1 emd_13048.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 212.70001 212.70001 212.70001 90.0 90.0 90.0 X Y Z -0.092141904 0.17856313 0.00033691214 0.009092562 1.0635 1.0635 1.0635 0.035 AUTHOR ::::EMDATABANK.org::::EMD-13048:::: post-processed sharpened map 6RX4 PDB experimental model FLEXIBLE FIT WEIGHTED MAP SUM AT ATOM CENTERS REAL 94.0