2025-04-09 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY REFINEMENT_DESCRIPTION database_2 em_3d_fitting_list em_admin pdbx_initial_refinement_model _database_2.pdbx_DOI _database_2.pdbx_database_accession _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 _em_admin.last_update DATABASE_REFERENCES citation _citation.journal_volume _citation.page_first _citation.page_last STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond database_2 em_3d_fitting_list em_admin pdbx_entry_details pdbx_initial_refinement_model pdbx_modification_feature struct_conn _database_2.pdbx_DOI _database_2.pdbx_database_accession _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 _em_admin.last_update _pdbx_entry_details.has_protein_modification _struct_conn.pdbx_leaving_atom_flag PDBe PDBe 2021-03-03 2021-04-21 2021-04-21 2025-04-09 Structure of the darobactin-bound E. coli BAM complex (BamABCDE) Jakob RP Kaur H Beta-Barrel, outer membrane, protein insertion, protein folding, protein maturation, antibiotic, natural product, cyclized peptide, MEMBRANE PROTEIN Kaur H Jakob RP Marzinek JK Green R Imai Y Bolla JR Agustoni E Robinson CV Bond PJ Lewis K Maier T Hiller S The antibiotic darobactin mimics a beta-strand to inhibit outer membrane insertase. Nature UK 593 125 129 2021 33854236 doi:10.1038/s41586-021-03455-w 1476-4687 0006 NATUAS 7nri FULLOVERLAP BamABCDE complex BamABCDE complex 0 2 3 4 5 Escherichia coli K-12 Outer membrane protein assembly factor BamA Escherichia coli (strain K12) K12 0.08822743 1 Escherichia coli BL21(DE3) LEVO AEGFVVKDIHFEGLQRVAVGAALLSMPVRTGDTVNDEDISNTIRALFATGNFEDVRVLRDGDTLLVQVKERPTIASITFS GNKSVKDDMLKQNLEASGVRVGESLDRTTIADIEKGLEDFYYSVGKYSASVKAVVTPLPRNRVDLKLVFQEGVSAEIQQI NIVGNHAFTTDELISHFQLRDEVPWWNVVGDRKYQKQKLAGDLETLRSYYLDRGYARFNIDSTQVSLTPDKKGIYVTVNI TEGDQYKLSGVEVSGNLAGHSAEIEQLTKIEPGELYNGTKVTKMEDDIKKLLGRYGYAYPRVQSMPEINDADKTVKLRVN VDAGNRFYVRKIRFEGNDTSKDAVLRREMRQMEGAWLGSDLVDQGKERLNRLGFFETVDTDTQRVPGSPDQVDVVYKVKE RNTGSFNFGIGYGTESGVSFQAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTVDGVSLGGRLFYNDFQADDAD LSDYTNKSYGTDVTLGFPINEYNSLRAGLGYVHNSLSNMQPQVAMWRYLYSMGEHPSTSDQDNSFKTDDFTFNYGWTYNK LDRGYFPTDGSRVNLTGKVTIPGSDNEYYKVTLDTATYVPIDDDHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGSSTV RGFQSNTIGPKAVYFPHQASNYDPDYDYECATQDGAKDLCKSDDAVGGNAMAVASLEFITPTPFISDKYANSVRTSFFWD MGTVWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWMSPLGPLVFSYAQPFKKYDGDKAEQFQFNIGK P0A940 Outer membrane protein assembly factor BamB Escherichia coli (strain K12) K12 0.040924516 1 Escherichia coli BL21(DE3) LEVO CSLFNSEEDVVKMSPLPTVENQFTPTTAWSTSVGSGIGNFYSNLHPALADNVVYAADRAGLVKALNADDGKEIWSVSLAE KDGWFSKEPALLSGGVTVSGGHVYIGSEKAQVYALNTSDGTVAWQTKVAGEALSRPVVSDGLVLIHTSNGQLQALNEADG AVKWTVNLDMPSLSLRGESAPTTAFGAAVVGGDNGRVSAVLMEQGQMIWQQRISQATGSTEIDRLSDVDTTPVVVNGVVF ALAYNGNLTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVDQNDRVMALTIDGGVTLWTQSDLLHRLLTSPVLYNGNLVV GDSEGYLHWINVEDGRFVAQQKVDSSGFQTEPVAADGKLLIQAKDGTVYSITRWSHPQFEK P77774 Outer membrane protein assembly factor BamC Escherichia coli (strain K12) K12 0.03440125 1 Escherichia coli BL21(DE3) LEVO CSSDSRYKRQVSGDEAYLEAAPLAELHAPAGMILPVTSGDYAIPVTNGSGAVGKALDIRPPAQPLALVSGARTQFTGDTA SLLVENGRGNTLWPQVVSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLNLEQA GKPVADAASMQRYSTEMMNVISAGLDKSATDAANAAQNRASTTMDVQSAADDTGLPMLVVRGPFNVVWQRLPAALEKVGM KVTDSTRSQGNMAVTYKPLSDSDWQELGASDPGLASGDYKLQVGDLDNRSSLQFIDPKGHTLTQSQNDALVAVFQAAFSK P0A903 Outer membrane protein assembly factor BamD Escherichia coli (strain K12) K12 0.025816818 1 Escherichia coli BL21(DE3) LEVO CSGSKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLN PTHPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEY SVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNT P0AC02 Outer membrane protein assembly factor BamE Escherichia coli (strain K12) K12 0.011462772 1 Escherichia coli BL21(DE3) LEVO CSTLERVVYRPDINQGNYLTANDVSKIRVGMTQQQVAYALGTPLMSDPFGTNTWFYVFRQQPGHEGVTQQTLTLTFNSSG VLTNIDNKPALSGNKLHHHHHH P0A937 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE synthetic construct 0.000971047
Darobactin
1 LEVO WN(UX8)SKSF singleParticle particle 5.5 8.0 20.0 Tris 150.0 NaCl sodium chloride 0.05 DDM C-flat-1.2/1.3 COPPER 200 CARBON HOLEY 20.0 GLOW DISCHARGE AIR ETHANE 100 293 FEI VITROBOT MARK III
4microL of sample applied.
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 0.8 0.5 1.8 2.2 165000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20
Manually grid screening, operated by SerialEM
GATAN K2 SUMMIT (4k x 4k) COUNTING 1 5527 9.0 50.0 1 870023
cryoSpARC ab intio reconstruction
 1 C1 3.03 FSC 0.143 CUT-OFF cryoSPARC 157474 PROJECTION MATCHING cryoSPARC OTHER cryoSPARC emd_12546.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 420 420 420 0 0 0 420 420 420 344.4 344.4 344.4 90.0 90.0 90.0 X Y Z -0.20497094 0.64656365 0.0005612175 0.011930545 0.82 0.82 0.82 0.0305 AUTHOR 5D0O PDB experimental model AB INITIO MODEL REAL emd_12546_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 420 420 420 0 0 0 420 420 420 344.4 344.4 344.4 90.0 90.0 90.0 X Y Z -0.6199387 1.2758858 0.0005612174 0.020646533 0.82 0.82 0.82 AUTHOR sharpened_map (B-Factor of 51.2) emd_12546_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 420 420 420 0 0 0 420 420 420 344.4 344.4 344.4 90.0 90.0 90.0 X Y Z -0.82301843 0.83053625 0.0005689162 0.09366194 0.82 0.82 0.82 AUTHOR half_map_B emd_12546_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 420 420 420 0 0 0 420 420 420 344.4 344.4 344.4 90.0 90.0 90.0 X Y Z -0.77744913 0.843474 0.00055863586 0.093712114 0.82 0.82 0.82 AUTHOR half_map_A