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 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 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 PDBe PDBe 2019-02-22 2021-01-20 2021-01-20 2025-04-09 Research Council of Norway Norway Research Council of Norway 275207 Norway National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R01AI78000 United States Helicobacter pylori urease with BME bound in the active site Luecke H Cunha E dodecamer, bi nickel center, enzyme, cytoplasm, HYDROLASE Cunha ES Chen X Sanz-Gaitero M Mills DJ Luecke H Cryo-EM structure of Helicobacter pylori urease with an inhibitor in the active site at 2.0 angstrom resolution. Nat Commun UK 12 230 230 2021 33431861 doi:10.1038/s41467-020-20485-6 2041-1723 6qsu FULLOVERLAP 1.1 MDa Helicobacter pylori Urease 1.1 MDa Helicobacter pylori Urease 0 1 2 Helicobacter pylori UMAB41 Cytoplasm 1.1 Urease subunit alpha Helicobacter pylori 0.026645703 12 Escherichia coli LEVO MKLTPKELDKLMLHYAGELARKRKEKGIKLNYVEAVALISAHIMEEARAGKKTAAELMQEGRTLLKPDDVMDGVASMIHE VGIEAMFPDGTKLVTVHTPIEANGKLVPGELFLKNEDITINEGKKAVSVKVKNVGDRPVQIGSHFHFFEVNRCLDFDREK TFGKRLDIASGTAVRFEPGEEKSVELIDIGGNRRIFGFNALVDRQADNESKKIALHRAKERGFHGTKSDDNYVKTIKE A0A293SGE9 3.5.1.5 Urease subunit beta Helicobacter pylori 0.061832531 12 Escherichia coli LEVO MKKISRKEYVSMYGPTTGDKVRLGDTDLIAEVEHDYTIYGEELKFGGGKTLREGMSQSNNPSKEELDLIITNALIVDYTG IYKADIGIKDGKIAGIGKGGNKDMQDGVKNNLSVGPATEALAGEGLIVTAGGIDTHIHFISPQQIPTAFASGVTTMIGGG TGPADGTNATTITPGRRNLKWMLRAAEEYSMNLGFLAKGNTSNDASLADQIEAGAIGF(KCX)IHEDWGTTPSAINHALD VADKYDVQVAIHTDTLNEAGCVEDTMAAIAGRTMHTFHTEGAGGGHAPDIIKVAGEHNILPASTNPTIPFTVNTEAEHMD MLMVCHHLDKSIKEDVQFADSRIRPQTIAAEDTLHDMGIFSITSSDSQAMGRVGEVITRTWQTADKNKKEFGRLKEEKGD NDNFRIKRYLSKYTINPAIAHGISEYVGSVEVGKVADLVLWSPAFFGVKPNMIIKGGFIALSQMGDANASIPTPQPVYYR EMFAHHGKAKYDANITFVSQAAYDKGIKEELGLERQVLPVKNCRNITKKDMQFNDTTAHIEVNPETYHVFVDGKEVTSKP ANKVSLAQLFSIF A0A086RWB6 3.5.1.5 NICKEL (II) ION 5.8692999999999995e-05 24 NI BETA-MERCAPTOETHANOL 7.813299999999999e-05 12 BME water 1.8015e-05 1178 HOH singleParticle particle 2 8.0 20.0 Hepes 1.0 EDTA 1.0 BME Quantifoil R2/2 COPPER GLOW DISCHARGE ETHANE 70 283 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) 1 956 50.0
Used 718 movies
 GATAN K2 SUMMIT (4k x 4k) 40.0 GATAN K2 SUMMIT (4k x 4k) 40.0 1 203000 1E9Z
3.0 A crystal structure of apo form
 1 T 2.4 FSC 0.143 CUT-OFF RELION 3.0 beta 175895 NOT APPLICABLE RELION 3.0 beta NOT APPLICABLE RELION 3.0 beta 6 28000.0 RELION 3.0 beta emd_4629.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 323.1 323.1 323.1 90.0 90.0 90.0 X Y Z -0.15039964 0.26389554 0.00031169914 0.010078388 1.077 1.077 1.077 0.05 AUTHOR unmasked map 1E9Z A PDB experimental model 1E9Z B PDB experimental model RIGID BODY FIT REAL emd_4629_msk_1.map emd_4629_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 153 157 153 77 73 74 153 157 153 164.781 169.089 164.781 90.0 90.0 90.0 Z Y X -1.7167628 2.4176128 0.000000000001052 0.21985471 1.077 1.077 1.077 AUTHOR density modified map emd_4629_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 323.1 323.1 323.1 90.0 90.0 90.0 X Y Z -0.02332859 0.06580606 -0.00003422834 0.0034706625 1.077 1.077 1.077 AUTHOR half map emd_4629_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 323.1 323.1 323.1 90.0 90.0 90.0 X Y Z -0.024895346 0.06387592 -0.00003424954 0.0034768682 1.077 1.077 1.077 AUTHOR half map