2026-08-12 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond em_admin pdbx_entry_details pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order pdbx_validate_chiral _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.value_order _em_admin.last_update _pdbx_entry_details.has_protein_modification EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update RCSB RCSB 2023-09-11 2024-04-24 2024-04-24 2026-08-12 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 5R35GM133325-04 United States Klebsiella pneumoniae encapsulin-associated DyP peroxidase Andreas MP Jones JA Giessen TW DyP peroxidase, encapsulin, OXIDOREDUCTASE Jones JA Andreas MP Giessen TW Structural basis for peroxidase encapsulation inside the encapsulin from the Gram-negative pathogen Klebsiella pneumoniae. Nat Commun UK 15 2558 2558 2024 38519509 doi:10.1038/s41467-024-46880-x 2041-1723 8u4z FULLOVERLAP EMDB EMD-41904 associated EM volume
Klebsiella pneumoniae encapsulin-associated DyP peroxidase
 Klebsiella pneumoniae family 1 encapsulin-associated DyP peroxidase Klebsiella pneumoniae family 1 encapsulin-associated DyP peroxidase 0 1 Klebsiella pneumoniae 0.24 Family 1 encapsulin-associated DyP peroxidase Klebsiella pneumoniae 0.040691395
Residues 1-352 are K.p. DyP peroxidase (NCBI: WP_193221875.1). Residues 1-2 and 316-352 are disordered. Residues 353-370 are a TEV protease site, linker, and HIS-tag that are disordered in the structure.
1 Escherichia coli BL21(DE3) LEVO MACPISQSVSQPVDERLTRAAIFLVVTINPGKAAEVAVRTLCGTLSSLVRGVGFRILDGGLSCVMGVSSGGWERLFGDEK PEYLHVFQEINGVHHAPSTPGDLLFHIRAARMDLCFELASRILSDLGSSVCVVDSVQGFRYFDDRDLLGFVDGTENPVAQ AAVDATLIGEEDHTFSGGSYVIVQKYLHDLDKWNAIPVEQQEKIIGREKLSDIELKDADKPSYAHNVLTSIEEDGEDVDI LRDNMPFGDPGKGEFGTYFIGYSRKPARIERMLENMFVGNPPGNYDRILDVSRAITGTLFFIPTVSFLDSVEPQPSVSQQ TDDAKYIYDSPGTKGESGSLNIGSLKKEVQDEENLYFQGGSGGHHHHHHH Mesoheme 0.0006205189999999999 1 MH0 singleParticle particle 0.45 7.5 20.0 C4H12NO3 Tris 150.0 NaCl Sodium chloride
20 mM Tris pH 7.5, 150 mM NaCl
 Quantifoil R2/1 COPPER 200 CARBON HOLEY GLOW DISCHARGE AIR
60 seconds at 5 mA
 ETHANE 100 295 FEI VITROBOT MARK IV
Blot force: 5 Blot time: 2 seconds.
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 0.8 1.8 105000.0 NITROGEN GATAN K3 BIOQUANTUM (6k x 4k) COUNTING 5760 4092 1 2468 1.89747 50.02 1 2603020 cryoSPARC 4.4.0+231114 Patch CTF Estimation in cryoSPARC Live PHASE FLIPPING AND AMPLITUDE CORRECTION Ab initio model D3 2.39 FSC 0.143 CUT-OFF cryoSPARC 4.4.0+231114 Local Refinement
Unmasked local refinement was performed with D3 symmetry imposed.
431317 MAXIMUM LIKELIHOOD cryoSPARC 4.4.0+231114 MAXIMUM LIKELIHOOD cryoSPARC 4.4.0+231114 emd_41904.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 212.992 212.992 212.992 90.0 90.0 90.0 X Y Z -0.3818379 0.6607309 0.00031092373 0.020920508 0.832 0.832 0.832 0.06 AUTHOR Klebsiella pneumoniae encapsulin-associated DyP peroxidase AF-A0A3Z8UGY6-F1 Other in silico model
An AlphaFill model containing bound heme was used as starting model
 FLEXIBLE FIT
Initial fitting was performed using ChimeraX v1.2.5. The model was then manually refined and mutated using Coot v9.8.1 followed by real-space refinement using Phenix v1.20.1-4487-000.
Cross-correlation coefficient REAL 107.700000000000003 emd_41904_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 212.992 212.992 212.992 90.0 90.0 90.0 X Y Z -0.06383683 0.15204246 0.00027753206 0.0077386657 0.832 0.832 0.832 AUTHOR Half Map A emd_41904_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 212.992 212.992 212.992 90.0 90.0 90.0 X Y Z -0.068233214 0.15476035 0.00027619928 0.0077411206 0.832 0.832 0.832 AUTHOR Half Map B