2024-05-22 REL PDBe PDBe PDBe 2019-06-07 2019-10-16 2019-11-20 2024-05-22 German Research Foundation Germany THE STRUCTURE OF BD OXIDASE FROM ESCHERICHIA COLI Rasmussen T Boettcher B BD OXIDASE, TERMINAL OXIDASE, OXIDOREDUCTASE Thesseling A Rasmussen T Burschel S Wohlwend D Kagi J Muller R Bottcher B Friedrich T Homologous bd oxidases share the same architecture but differ in mechanism. Nat Commun UK 10 5138 5138 2019 31723136 doi:10.1038/s41467-019-13122-4 2041-1723 6rx4 FULLOVERLAP bd-oxidase from Escherichia coli bd-oxidase from Escherichia coli 0 1 2 3 4
Reconstruction into Amphipole A8-35 in the presence of the inhibitor aurachin C.
Escherichia coli K-12 Cytochrome bd-I ubiquinol oxidase subunit 1 Escherichia coli (strain K12) 0.058251723 1 LEVO MLDIVELSRLQFALTAMYHFLFVPLTLGMAFLLAIMETVYVLSGKQIYKDMTKFWGKLFGINFALGVATGLTMEFQFGTN WSYYSHYVGDIFGAPLAIEGLMAFFLESTFVGLFFFGWDRLGKVQHMCVTWLVALGSNLSALWILVANGWMQNPIASDFN FETMRMEMVSFSELVLNPVAQVKFVHTVASGYVTGAMFILGISAWYMLKGRDFAFAKRSFAIAASFGMAAVLSVIVLGDE SGYEMGDVQKTKLAAIEAEWETQPAPAAFTLFGIPDQEEETNKFAIQIPYALGIIATRSVDTPVIGLKELMVQHEERIRN GMKAYSLLEQLRSGSTDQAVRDQFNSMKKDLGYGLLLKRYTPNVADATEAQIQQATKDSIPRVAPLYFAFRIMVACGFLL LAIIALSFWSVIRNRIGEKKWLLRAALYGIPLPWIAVEAGWFVAEYGRQPWAIGEVLPTAVANSSLTAGDLIFSMVLICG LYTLFLVAELFLMFKFARLGPSSLKTGRYHFEQSSTTTQPAR P0ABJ9 7.1.1.7 Cytochrome bd-I ubiquinol oxidase subunit 2 Escherichia coli (strain K12) 0.042479828 1 LEVO MIDYEVLRFIWWLLVGVLLIGFAVTDGFDMGVGMLTRFLGRNDTERRIMINSIAPHWDGNQVWLITAGGALFAAWPMVYA AAFSGFYVAMILVLASLFFRPVGFDYRSKIEETRWRNMWDWGIFIGSFVPPLVIGVAFGNLLQGVPFNVDEYLRLYYTGN FFQLLNPFGLLAGVVSVGMIITQGATYLQMRTVGELHLRTRATAQVAALVTLVCFALAGVWVMYGIDGYVVKSTMDHYAA SNPLNKEVVREAGAWLVNFNNTPILWAIPALGVVLPLLTILTARMDKAAWAFVFSSLTLACIILTAGIAMFPFVMPSSTM MNASLTMWDATSSQLTLNVMTWVAVVLVPIILLYTAWCYWKMFGRITKEDIERNTHSLY P0ABK2 7.1.1.7 Cytochrome bd-I ubiquinol oxidase subunit X Escherichia coli (strain K12) 0.004043662999999999 1 LEVO MWYFAWILGTLLACSFGVITALALEHVESGKAGQEDI P56100 7.1.1.7 Cytochrome bd-I ubiquinol oxidase subunit Y Escherichia coli K-12 0.002230741 1 LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) HEME B/C 0.0006185030000000001 2 HEB CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE 0.0006324869999999999 1 HDD 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine 0.000744034 1 PEE Ubiquinone-8 0.000727109 1 UQ8 water 1.8015e-05 7 HOH singleParticle particle 2 7.5 20.0 C7H15NO4S MOPS 20.0 NaCl sodium chloride Quantifoil R1.2/1.3 COPPER 400 CARBON HOLEY GLOW DISCHARGE AIR 0.0029300000000000003 ETHANE 100 277 FEI VITROBOT MARK IV
blot time 3.5 sec, blot force 5.
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 1.4000000000000001 2.2 75000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON III (4k x 4k) COUNTING 1 8663 75.0 59.0
Images were collected in movie mode with 47 frames.
 1
Movies were motion corrected and dose weighted with the program Motioncorr2.
C1 FOURIER SPACE 3.3 FSC 0.143 CUT-OFF RELION 3.0 197805 MAXIMUM LIKELIHOOD RELION 3.0 MAXIMUM LIKELIHOOD RELION 3.0 3 RELION 3.0 emd_10049.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 150 150 150 0 0 0 150 150 150 159.52501 159.52501 159.52501 90.0 90.0 90.0 X Y Z -0.12678012 0.22499055 0.0017706004 0.011363435 1.0635 1.0635 1.0635 0.052 AUTHOR sharpened map after postprocess (Relion) without mask 5DOQ PDB experimental model AB INITIO MODEL REAL 88.0 emd_10049_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 150 150 150 0 0 0 150 150 150 159.52501 159.52501 159.52501 90.0 90.0 90.0 X Y Z -0.028493129 0.12542583 0.0017722357 0.006809538 1.0635 1.0635 1.0635 AUTHOR unfiltered half map emd_10049_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 150 150 150 0 0 0 150 150 150 159.52501 159.52501 159.52501 90.0 90.0 90.0 X Y Z -0.02619548 0.12501182 0.0017689652 0.0068320017 1.0635 1.0635 1.0635 AUTHOR unfiltered half map