2026-09-02 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY em_admin pdbx_entry_details pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order _em_admin.last_update _pdbx_entry_details.has_protein_modification EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update PDBe PDBe 2022-10-28 2023-08-16 2023-08-16 2026-09-02 Wellcome Trust 108466/Z/15/Z United Kingdom Wellcome Trust 221524/Z/20/Z United Kingdom CryoEM structure of quinol-dependent Nitric Oxide Reductase (qNOR) from Alcaligenes xylosoxidans at 2.2 A resolution Flynn A Antonyuk SV Eady RR Muench SP Hasnain SS quinol-dependent Nitric Oxide Reductase, proton transfer, quinol binding, ubiquinol oxidase, MEMBRANE PROTEIN Flynn AJ Antonyuk SV Eady RR Muench SP Hasnain SS A 2.2 angstrom cryoEM structure of a quinol-dependent NO Reductase shows close similarity to respiratory oxidases. Nat Commun UK 14 3416 3416 2023 37296134 doi:10.1038/s41467-023-39140-x 2041-1723 8bgw FULLOVERLAP EMDB EMD-16041 associated EM volume
CryoEM structure of quinol-dependent Nitric Oxide Reductase (qNOR) from Alcaligenes xylosoxidans at 2.2 A resolution
 quinol-dependent Nitric Oxide Reductase quinol-dependent Nitric Oxide Reductase 0 1
quinol-dependent Nitric Oxide Reductase
Achromobacter xylosoxidans Nitric oxide reductase subunit B Achromobacter xylosoxidans 0.084724867 2 Escherichia coli BL21(DE3) LEVO MGPYRRLWFTLIAVLAVTFALLGFYGGEVYRQAPPIPEEVASADGTRLFGRDDILDGQTAWQSIGGMQLGSIWGHGAYQA PDWTADWLHRELMAWLDLAARDAHGRDYGQLDAPAQAALREQLKAEYRANRADAAGGKLTLSPRRAQAVAQTEAYYDQLF SDAPALHRSRENYAMKENTLPDANRRRQMTHFFFWTAWAAATEREGTSVTYTNNWPHEPLIGNHPSSENVMWSIISVVVL LAGIGLLIWAWAFLRGKEEDEPPAPARDPLTTFALTPSQRALGKYLFLVVALFGFQVLLGGFTAHYTVEGQKFYGIDLSQ WFPYSLVRTWHIQSALFWIATGFLAAGLFLAPLINGGRDPKYQKAGVDILFWALVLVVVGSFAGNYLAIAQIMPPDLNFW LGHQGYEYVDLGRLWQIGKFAGICFWLVLMLRGIVPALRTPGGDKNLLALLTASVGAIGLFYGAGFFYGERTHLTVMEYW RWWIVHLWVEGFFEVFATTALAFIFSTLGLVSRRMATTASLASASLFMLGGIPGTFHHLYFAGTTTPVMAVGASFSALEV VPLIVLGHEAWENWRLKTRAPWMENLKWPLMCFVAVAFWNMLGAGVFGFMINPPVSLYYIQGLNTTPVHAHAALFGVYGF LALGFTLLVLRYIRPQYALSPGLMKLAFWGLNLGLALMIFTSLLPIGLIQFHASVSEGMWYARSEAFMQQDILKTLRWGR TFGDVVFLLGALAMVVQVILGLLSGKPAAAEPVLRAEPARR A0A0D6H8R3 1.7.2.5 PROTOPORPHYRIN IX CONTAINING FE 0.000616487 4 HEM FE (III) ION 5.5845e-05 2 FE CALCIUM ION 4.0078e-05 2 CA decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside 0.000498628 2 10M UBIQUINONE-1 0.00025028999999999996 2 UQ1 (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE 0.0006618899999999999 13 LOP water 1.8015e-05 449 HOH singleParticle particle 3 7.0 50.0 Tris-HCL Tris-HCL
50mM Tris-HCl, 150mM NaCl, 0.05% DTM
 Quantifoil R1.2/1.3 GOLD 300 CARBON HOLEY GLOW DISCHARGE AIR ETHANE 100 277 FEI VITROBOT MARK IV
Sample at 3 mg/mL was applied to glow-discharged Quantifoil Au R1.2/1.3 holey carbo grids.
Sample was monodisperse
 FEI TITAN KRIOS SPOT SCAN BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.9 2.7 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 80.0 114.0 TFS Selectris 10 FEI FALCON IV (4k x 4k) 4096 4096 1 5466 6.11 34.9 1 3000000 CTFFIND 4.1 PHASE FLIPPING AND AMPLITUDE CORRECTION 6QQ5
Low-pass filtered to 60A for first 3D classification
 2 C2 FOURIER SPACE 2.2 FSC 0.143 CUT-OFF RELION 3.1 404950 MAXIMUM LIKELIHOOD RELION 3.1 MAXIMUM LIKELIHOOD RELION 3.1 6 121415.0 RELION 3.1 emd_16041.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 364.0 364.0 364.0 90.0 90.0 90.0 X Y Z -0.06622768 0.17982407 0.00004599626 0.0017005954 0.91 0.91 0.91 0.015 AUTHOR main map used for model building RIGID BODY FIT Cross-correlation coefficient RECIPROCAL 47.0 emd_16041_msk_1.map emd_16041_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 364.0 364.0 364.0 90.0 90.0 90.0 X Y Z -0.022367263 0.07389656 0.000014901217 0.0013119993 0.91 0.91 0.91 AUTHOR half map used for cross validation emd_16041_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 364.0 364.0 364.0 90.0 90.0 90.0 X Y Z -0.02165832 0.08018306 0.000015531557 0.0013146563 0.91 0.91 0.91 AUTHOR half map used in refinement