HEADER OXIDOREDUCTASE 11-SEP-23 8U4Z TITLE KLEBSIELLA PNEUMONIAE ENCAPSULIN-ASSOCIATED DYP PEROXIDASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FAMILY 1 ENCAPSULIN-ASSOCIATED DYP PEROXIDASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: RESIDUES 1-352 ARE K.P. DYP PEROXIDASE (NCBI: COMPND 6 WP_193221875.1). RESIDUES 1-2 AND 316-352 ARE DISORDERED. RESIDUES COMPND 7 353-370 ARE A TEV PROTEASE SITE, LINKER, AND HIS-TAG THAT ARE COMPND 8 DISORDERED IN THE STRUCTURE. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 GENE: GBV82_RS22370; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS DYP PEROXIDASE, ENCAPSULIN, OXIDOREDUCTASE EXPDTA ELECTRON MICROSCOPY AUTHOR M.P.ANDREAS,J.A.JONES,T.W.GIESSEN REVDAT 1 24-APR-24 8U4Z 0 JRNL AUTH J.A.JONES,M.P.ANDREAS,T.W.GIESSEN JRNL TITL STRUCTURAL BASIS FOR PEROXIDASE ENCAPSULATION INSIDE THE JRNL TITL 2 ENCAPSULIN FROM THE GRAM-NEGATIVE PATHOGEN KLEBSIELLA JRNL TITL 3 PNEUMONIAE. JRNL REF NAT COMMUN V. 15 2558 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 38519509 JRNL DOI 10.1038/S41467-024-46880-X REMARK 2 REMARK 2 RESOLUTION. 2.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, SERIALEM, CRYOSPARC, UCSF REMARK 3 CHIMERAX, COOT, PHENIX, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : CROSS-CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : 107.700 REMARK 3 REMARK 3 FITTING PROCEDURE : INITIAL FITTING WAS PERFORMED USING CHIMERAX REMARK 3 V1.2.5. THE MODEL WAS THEN MANUALLY REFINED AND MUTATED USING REMARK 3 COOT V9.8.1 FOLLOWED BY REAL-SPACE REFINEMENT USING PHENIX REMARK 3 V1.20.1-4487-000. REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 2.390 REMARK 3 NUMBER OF PARTICLES : 431317 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: UNMASKED LOCAL REFINEMENT WAS PERFORMED WITH D3 REMARK 3 SYMMETRY IMPOSED. REMARK 4 REMARK 4 8U4Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1000276730. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : KLEBSIELLA PNEUMONIAE FAMILY 1 REMARK 245 ENCAPSULIN-ASSOCIATED DYP REMARK 245 PEROXIDASE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.45 REMARK 245 SAMPLE SUPPORT DETAILS : 60 SECONDS AT 5 MA REMARK 245 SAMPLE VITRIFICATION DETAILS : BLOT FORCE: 5 BLOT TIME: 2 REMARK 245 SECONDS REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 2468 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5002.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 105000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 DIHEDRAL POINT SYMMETRY (SCHOENFLIES SYMBOL = D3). REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 SER A 316 REMARK 465 VAL A 317 REMARK 465 SER A 318 REMARK 465 GLN A 319 REMARK 465 GLN A 320 REMARK 465 THR A 321 REMARK 465 ASP A 322 REMARK 465 ASP A 323 REMARK 465 ALA A 324 REMARK 465 LYS A 325 REMARK 465 TYR A 326 REMARK 465 ILE A 327 REMARK 465 TYR A 328 REMARK 465 ASP A 329 REMARK 465 SER A 330 REMARK 465 PRO A 331 REMARK 465 GLY A 332 REMARK 465 THR A 333 REMARK 465 LYS A 334 REMARK 465 GLY A 335 REMARK 465 GLU A 336 REMARK 465 SER A 337 REMARK 465 GLY A 338 REMARK 465 SER A 339 REMARK 465 LEU A 340 REMARK 465 ASN A 341 REMARK 465 ILE A 342 REMARK 465 GLY A 343 REMARK 465 SER A 344 REMARK 465 LEU A 345 REMARK 465 LYS A 346 REMARK 465 LYS A 347 REMARK 465 GLU A 348 REMARK 465 VAL A 349 REMARK 465 GLN A 350 REMARK 465 ASP A 351 REMARK 465 GLU A 352 REMARK 465 GLU A 353 REMARK 465 ASN A 354 REMARK 465 LEU A 355 REMARK 465 TYR A 356 REMARK 465 PHE A 357 REMARK 465 GLN A 358 REMARK 465 GLY A 359 REMARK 465 GLY A 360 REMARK 465 SER A 361 REMARK 465 GLY A 362 REMARK 465 GLY A 363 REMARK 465 HIS A 364 REMARK 465 HIS A 365 REMARK 465 HIS A 366 REMARK 465 HIS A 367 REMARK 465 HIS A 368 REMARK 465 HIS A 369 REMARK 465 HIS A 370 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 315 C - N - CD ANGL. DEV. = -13.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 16 65.86 60.78 REMARK 500 PHE A 76 -164.19 -117.21 REMARK 500 PHE A 142 -137.30 59.73 REMARK 500 ALA A 159 -123.68 58.21 REMARK 500 ASP A 219 30.82 -98.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MH0 A 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 225 NE2 REMARK 620 2 MH0 A 401 NB 93.2 REMARK 620 3 MH0 A 401 NC 97.6 88.7 REMARK 620 4 MH0 A 401 NA 88.2 91.1 174.2 REMARK 620 5 MH0 A 401 ND 91.6 175.2 90.9 88.8 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-41904 RELATED DB: EMDB REMARK 900 KLEBSIELLA PNEUMONIAE ENCAPSULIN-ASSOCIATED DYP PEROXIDASE DBREF 8U4Z A 1 370 PDB 8U4Z 8U4Z 1 370 SEQRES 1 A 370 MET ALA CYS PRO ILE SER GLN SER VAL SER GLN PRO VAL SEQRES 2 A 370 ASP GLU ARG LEU THR ARG ALA ALA ILE PHE LEU VAL VAL SEQRES 3 A 370 THR ILE ASN PRO GLY LYS ALA ALA GLU VAL ALA VAL ARG SEQRES 4 A 370 THR LEU CYS GLY THR LEU SER SER LEU VAL ARG GLY VAL SEQRES 5 A 370 GLY PHE ARG ILE LEU ASP GLY GLY LEU SER CYS VAL MET SEQRES 6 A 370 GLY VAL SER SER GLY GLY TRP GLU ARG LEU PHE GLY ASP SEQRES 7 A 370 GLU LYS PRO GLU TYR LEU HIS VAL PHE GLN GLU ILE ASN SEQRES 8 A 370 GLY VAL HIS HIS ALA PRO SER THR PRO GLY ASP LEU LEU SEQRES 9 A 370 PHE HIS ILE ARG ALA ALA ARG MET ASP LEU CYS PHE GLU SEQRES 10 A 370 LEU ALA SER ARG ILE LEU SER ASP LEU GLY SER SER VAL SEQRES 11 A 370 CYS VAL VAL ASP SER VAL GLN GLY PHE ARG TYR PHE ASP SEQRES 12 A 370 ASP ARG ASP LEU LEU GLY PHE VAL ASP GLY THR GLU ASN SEQRES 13 A 370 PRO VAL ALA GLN ALA ALA VAL ASP ALA THR LEU ILE GLY SEQRES 14 A 370 GLU GLU ASP HIS THR PHE SER GLY GLY SER TYR VAL ILE SEQRES 15 A 370 VAL GLN LYS TYR LEU HIS ASP LEU ASP LYS TRP ASN ALA SEQRES 16 A 370 ILE PRO VAL GLU GLN GLN GLU LYS ILE ILE GLY ARG GLU SEQRES 17 A 370 LYS LEU SER ASP ILE GLU LEU LYS ASP ALA ASP LYS PRO SEQRES 18 A 370 SER TYR ALA HIS ASN VAL LEU THR SER ILE GLU GLU ASP SEQRES 19 A 370 GLY GLU ASP VAL ASP ILE LEU ARG ASP ASN MET PRO PHE SEQRES 20 A 370 GLY ASP PRO GLY LYS GLY GLU PHE GLY THR TYR PHE ILE SEQRES 21 A 370 GLY TYR SER ARG LYS PRO ALA ARG ILE GLU ARG MET LEU SEQRES 22 A 370 GLU ASN MET PHE VAL GLY ASN PRO PRO GLY ASN TYR ASP SEQRES 23 A 370 ARG ILE LEU ASP VAL SER ARG ALA ILE THR GLY THR LEU SEQRES 24 A 370 PHE PHE ILE PRO THR VAL SER PHE LEU ASP SER VAL GLU SEQRES 25 A 370 PRO GLN PRO SER VAL SER GLN GLN THR ASP ASP ALA LYS SEQRES 26 A 370 TYR ILE TYR ASP SER PRO GLY THR LYS GLY GLU SER GLY SEQRES 27 A 370 SER LEU ASN ILE GLY SER LEU LYS LYS GLU VAL GLN ASP SEQRES 28 A 370 GLU GLU ASN LEU TYR PHE GLN GLY GLY SER GLY GLY HIS SEQRES 29 A 370 HIS HIS HIS HIS HIS HIS HET MH0 A 401 43 HETNAM MH0 MESOHEME FORMUL 2 MH0 C34 H36 FE N4 O4 HELIX 1 AA1 SER A 10 ARG A 16 1 7 HELIX 2 AA2 GLY A 31 PHE A 54 1 24 HELIX 3 AA3 SER A 68 PHE A 76 1 9 HELIX 4 AA4 ARG A 111 ASP A 125 1 15 HELIX 5 AA5 LEU A 126 SER A 128 5 3 HELIX 6 AA6 ALA A 159 LEU A 167 1 9 HELIX 7 AA7 GLY A 169 SER A 176 5 8 HELIX 8 AA8 ASP A 189 ILE A 196 1 8 HELIX 9 AA9 PRO A 197 GLY A 206 1 10 HELIX 10 AB1 LYS A 216 LYS A 220 5 5 HELIX 11 AB2 ALA A 224 THR A 229 1 6 HELIX 12 AB3 LYS A 265 VAL A 278 1 14 HELIX 13 AB4 ARG A 287 VAL A 291 1 5 HELIX 14 AB5 THR A 304 SER A 310 1 7 SHEET 1 AA1 4 SER A 62 VAL A 67 0 SHEET 2 AA1 4 LEU A 103 ALA A 109 -1 O ARG A 108 N SER A 62 SHEET 3 AA1 4 ALA A 20 ILE A 28 -1 N ALA A 20 O ALA A 109 SHEET 4 AA1 4 VAL A 130 PHE A 139 -1 O ASP A 134 N VAL A 25 SHEET 1 AA2 2 ILE A 90 ASN A 91 0 SHEET 2 AA2 2 HIS A 95 ALA A 96 -1 O ALA A 96 N ILE A 90 SHEET 1 AA3 3 LEU A 241 ARG A 242 0 SHEET 2 AA3 3 GLU A 254 SER A 263 -1 O TYR A 262 N LEU A 241 SHEET 3 AA3 3 MET A 245 ASP A 249 -1 N MET A 245 O TYR A 258 SHEET 1 AA4 4 LEU A 241 ARG A 242 0 SHEET 2 AA4 4 GLU A 254 SER A 263 -1 O TYR A 262 N LEU A 241 SHEET 3 AA4 4 SER A 179 HIS A 188 -1 N HIS A 188 O PHE A 255 SHEET 4 AA4 4 SER A 292 ILE A 302 -1 O ILE A 302 N SER A 179 SHEET 1 AA5 2 GLU A 232 GLU A 233 0 SHEET 2 AA5 2 GLU A 236 ASP A 237 -1 O GLU A 236 N GLU A 233 LINK NE2 HIS A 225 FE MH0 A 401 1555 1555 2.11 CISPEP 1 ASN A 280 PRO A 281 0 19.24 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000