2025-04-09 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY 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 _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 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 PDBe PDBe 2020-04-10 2021-01-13 2021-01-13 2025-04-09 European Research Council (ERC) Chap4Resp European Molecular Biology Organization (EMBO) ALTF441-2017 Marie Sklodowska-Curie Actions, FragNET ITN RespViRALI Inducible lysine decarboxylase LdcI stacks, pH 5.7 Felix J Jessop M Acid stress-inducible, decarboxylase, LAOdc, LYASE Jessop M Liesche C Felix J Desfosses A Baulard M Adam V Fraudeau A Huard K Effantin G Kleman JP Bacia-Verloop M Bourgeois D Gutsche I Supramolecular assembly of the Escherichia coli LdcI upon acid stress. Proc.Natl.Acad.Sci.USA US 118 2021 33372137 doi:10.1073/pnas.2014383118 1091-6490 0040 PNASA6 EMD-10849 other EM volume 6yn6 FULLOVERLAP E. coli inducible lysine decarboxylase at pH 5.7 E. coli inducible lysine decarboxylase at pH 5.7 0 1 Escherichia coli K-12 Inducible lysine decarboxylase Escherichia coli (strain K12) K12 0.08111057 20 Escherichia coli str. K-12 substr. MG1655 LEVO MNVIAILNHMGVYFKEEPIRELHRALERLNFQIVYPNDRDDLLKLIENNARLCGVIFDWDKYNLELCEEISKMNENLPLY AFANTYSTLDVSLNDLRLQISFFEYALGAAEDIANKIKQTTDEYINTILPPLTKALFKYVREGKYTFCTPGHMGGTAFQK SPVGSLFYDFFGPNTMKSDISISVSELGSLLDHSGPHKEAEQYIARVFNADRSYMVTNGTSTANKIVGMYSAPAGSTILI DRNCHKSLTHLMMMSDVTPIYFRPTRNAYGILGGIPQSEFQHATIAKRVKETPNATWPVHAVITNSTYDGLLYNTDFIKK TLDVKSIHFDSAWVPYTNFSPIYEGKCGMSGGRVEGKVIYETQSTH(LLP)LLAAFSQASMIHVKGDVNEETFNEAYMMH TTTSPHYGIVASTETAAAMMKGNAGKRLINGSIERAIKFRKEIKRLRTESDGWFFDVWQPDHIDTTECWPLRSDSTWHGF KNIDNEHMYLDPIKVTLLTPGMEKDGTMSDFGIPASIVAKYLDEHGIVVEKTGPYNLLFLFSIGIDKTKALSLLRALTDF KRAFDLNLRVKNMLPSLYREDPEFYENMRIQELAQNIHKLIVHHNLPDLMYRAFEVLPTMVMTPYAAFQKELHGMTEEVY LDEMVGRINANMILPYPPGVPLVMPGEMITEESRPVLEFLQMLCEIGAHYPGFETDIHGAYRQADGRYTVKVLKE P0A9H3 4.1.1.18 singleParticle filament 0.25 5.7 Quantifoil R2/1 COPPER 300 CARBON HOLEY GLOW DISCHARGE ETHANE 100 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER GIF Bioquantum 20 GATAN K2 SUMMIT (4k x 4k) COUNTING 2564 6.0 29.3 1 15165 3N75
Initial model generated by manually stacking three LdcI decamers (PDB ID: 3N75) in Chimera and low-pass filtering the resulting LdcI-stack to 40 A.
 D5 3.28 FSC 0.143 CUT-OFF cryoSPARC 15157 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC emd_10850.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 336.64 336.64 336.64 90.0 90.0 90.0 X Y Z -1.7729001 2.9629934 0.024371587 0.19197333 1.052 1.052 1.052 0.6 AUTHOR LdcI stack, post-processed map. 3N75 PDB experimental model REAL 96.0 emd_10850_msk_1.map emd_10850_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 336.64 336.64 336.64 90.0 90.0 90.0 X Y Z -1.1624473 1.7328466 0.0105895195 0.19575952 1.052 1.052 1.052 AUTHOR LdcI stack, half map 1. emd_10850_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 336.64 336.64 336.64 90.0 90.0 90.0 X Y Z -1.1893679 1.6659127 0.010651374 0.19777647 1.052 1.052 1.052 AUTHOR LdcI stack, half map 2.