HEADER OXIDOREDUCTASE 17-JUL-23 8PVD TITLE STRUCTURE OF CATALASE DETERMINED BY CRYOEM AT 100 KEV COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATALASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.11.1.6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CAT; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS OXIDOREDUCTASE EXPDTA ELECTRON MICROSCOPY AUTHOR G.MCMULLAN,K.NAYDENOVA,D.MIHAYLOV,M.J.PEET,H.WILSON,K.YAMASHITA, AUTHOR 2 J.L.DICKERSON,S.CHEN,G.CANNONE,Y.LEE,K.A.HUTCHINGS,O.GITTINS, AUTHOR 3 M.SOBHY,T.WELLS,M.M.EL-GOMATI,J.DALBY,M.MEFFERT,C.SCHULZE-BRIESE, AUTHOR 4 R.HENDERSON,C.J.RUSSO REVDAT 2 06-DEC-23 8PVD 1 JRNL REVDAT 1 29-NOV-23 8PVD 0 JRNL AUTH G.MCMULLAN,K.NAYDENOVA,D.MIHAYLOV,K.YAMASHITA,M.J.PEET, JRNL AUTH 2 H.WILSON,J.L.DICKERSON,S.CHEN,G.CANNONE,Y.LEE,K.A.HUTCHINGS, JRNL AUTH 3 O.GITTINS,M.A.SOBHY,T.WELLS,M.M.EL-GOMATI,J.DALBY,M.MEFFERT, JRNL AUTH 4 C.SCHULZE-BRIESE,R.HENDERSON,C.J.RUSSO JRNL TITL STRUCTURE DETERMINATION BY CRYOEM AT 100 KEV. JRNL REF PROC.NATL.ACAD.SCI.USA V. 120 05120 2023 JRNL REFN ESSN 1091-6490 JRNL PMID 38011573 JRNL DOI 10.1073/PNAS.2312905120 REMARK 2 REMARK 2 RESOLUTION. 3.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SERVALCAT REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 7P8W REMARK 3 REFINEMENT SPACE : RECIPROCAL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL 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) : 3.400 REMARK 3 NUMBER OF PARTICLES : 27165 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: NULL REMARK 4 REMARK 4 8PVD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1292131834. 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 : CATALASE FROM HUMAN REMARK 245 ERYTHROCYTES REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : JEOL 1400/HR + YPS FEG REMARK 245 DETECTOR TYPE : DECTRIS SINGLA (1K X 1K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 100 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 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 211.32800 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 211.32800 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 211.32800 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 211.32800 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 211.32800 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 211.32800 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 ASP A 3 REMARK 465 LYS A 506 REMARK 465 ASN A 507 REMARK 465 ALA A 508 REMARK 465 ILE A 509 REMARK 465 HIS A 510 REMARK 465 THR A 511 REMARK 465 PHE A 512 REMARK 465 VAL A 513 REMARK 465 GLN A 514 REMARK 465 SER A 515 REMARK 465 GLY A 516 REMARK 465 SER A 517 REMARK 465 HIS A 518 REMARK 465 LEU A 519 REMARK 465 ALA A 520 REMARK 465 ALA A 521 REMARK 465 ARG A 522 REMARK 465 GLU A 523 REMARK 465 LYS A 524 REMARK 465 ALA A 525 REMARK 465 ASN A 526 REMARK 465 LEU A 527 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 ALA A 20 -115.13 64.27 REMARK 500 ASP A 140 37.22 -90.31 REMARK 500 LYS A 169 -142.63 -105.99 REMARK 500 SER A 217 -52.52 73.64 REMARK 500 VAL A 313 -54.85 -128.44 REMARK 500 VAL A 329 -51.01 -123.62 REMARK 500 PRO A 347 30.56 -81.46 REMARK 500 ASP A 389 -144.06 77.34 REMARK 500 GLN A 395 -137.40 49.48 REMARK 500 PRO A 412 150.93 -46.59 REMARK 500 ASP A 437 -135.88 -85.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 68 0.07 SIDE CHAIN 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 HEM A 602 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 358 OH REMARK 620 2 HEM A 602 NA 92.6 REMARK 620 3 HEM A 602 NB 84.9 88.1 REMARK 620 4 HEM A 602 NC 88.9 175.4 87.7 REMARK 620 5 HEM A 602 ND 92.9 95.1 176.2 89.2 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-17962 RELATED DB: EMDB REMARK 900 STRUCTURE OF CATALASE DETERMINED BY CRYOEM AT 100 KEV DBREF 8PVD A 1 527 UNP P04040 CATA_HUMAN 1 527 SEQRES 1 A 527 MET ALA ASP SER ARG ASP PRO ALA SER ASP GLN MET GLN SEQRES 2 A 527 HIS TRP LYS GLU GLN ARG ALA ALA GLN LYS ALA ASP VAL SEQRES 3 A 527 LEU THR THR GLY ALA GLY ASN PRO VAL GLY ASP LYS LEU SEQRES 4 A 527 ASN VAL ILE THR VAL GLY PRO ARG GLY PRO LEU LEU VAL SEQRES 5 A 527 GLN ASP VAL VAL PHE THR ASP GLU MET ALA HIS PHE ASP SEQRES 6 A 527 ARG GLU ARG ILE PRO GLU ARG VAL VAL HIS ALA LYS GLY SEQRES 7 A 527 ALA GLY ALA PHE GLY TYR PHE GLU VAL THR HIS ASP ILE SEQRES 8 A 527 THR LYS TYR SER LYS ALA LYS VAL PHE GLU HIS ILE GLY SEQRES 9 A 527 LYS LYS THR PRO ILE ALA VAL ARG PHE SER THR VAL ALA SEQRES 10 A 527 GLY GLU SER GLY SER ALA ASP THR VAL ARG ASP PRO ARG SEQRES 11 A 527 GLY PHE ALA VAL LYS PHE TYR THR GLU ASP GLY ASN TRP SEQRES 12 A 527 ASP LEU VAL GLY ASN ASN THR PRO ILE PHE PHE ILE ARG SEQRES 13 A 527 ASP PRO ILE LEU PHE PRO SER PHE ILE HIS SER GLN LYS SEQRES 14 A 527 ARG ASN PRO GLN THR HIS LEU LYS ASP PRO ASP MET VAL SEQRES 15 A 527 TRP ASP PHE TRP SER LEU ARG PRO GLU SER LEU HIS GLN SEQRES 16 A 527 VAL SER PHE LEU PHE SER ASP ARG GLY ILE PRO ASP GLY SEQRES 17 A 527 HIS ARG HIS MET ASN GLY TYR GLY SER HIS THR PHE LYS SEQRES 18 A 527 LEU VAL ASN ALA ASN GLY GLU ALA VAL TYR CYS LYS PHE SEQRES 19 A 527 HIS TYR LYS THR ASP GLN GLY ILE LYS ASN LEU SER VAL SEQRES 20 A 527 GLU ASP ALA ALA ARG LEU SER GLN GLU ASP PRO ASP TYR SEQRES 21 A 527 GLY ILE ARG ASP LEU PHE ASN ALA ILE ALA THR GLY LYS SEQRES 22 A 527 TYR PRO SER TRP THR PHE TYR ILE GLN VAL MET THR PHE SEQRES 23 A 527 ASN GLN ALA GLU THR PHE PRO PHE ASN PRO PHE ASP LEU SEQRES 24 A 527 THR LYS VAL TRP PRO HIS LYS ASP TYR PRO LEU ILE PRO SEQRES 25 A 527 VAL GLY LYS LEU VAL LEU ASN ARG ASN PRO VAL ASN TYR SEQRES 26 A 527 PHE ALA GLU VAL GLU GLN ILE ALA PHE ASP PRO SER ASN SEQRES 27 A 527 MET PRO PRO GLY ILE GLU ALA SER PRO ASP LYS MET LEU SEQRES 28 A 527 GLN GLY ARG LEU PHE ALA TYR PRO ASP THR HIS ARG HIS SEQRES 29 A 527 ARG LEU GLY PRO ASN TYR LEU HIS ILE PRO VAL ASN CYS SEQRES 30 A 527 PRO TYR ARG ALA ARG VAL ALA ASN TYR GLN ARG ASP GLY SEQRES 31 A 527 PRO MET CYS MET GLN ASP ASN GLN GLY GLY ALA PRO ASN SEQRES 32 A 527 TYR TYR PRO ASN SER PHE GLY ALA PRO GLU GLN GLN PRO SEQRES 33 A 527 SER ALA LEU GLU HIS SER ILE GLN TYR SER GLY GLU VAL SEQRES 34 A 527 ARG ARG PHE ASN THR ALA ASN ASP ASP ASN VAL THR GLN SEQRES 35 A 527 VAL ARG ALA PHE TYR VAL ASN VAL LEU ASN GLU GLU GLN SEQRES 36 A 527 ARG LYS ARG LEU CYS GLU ASN ILE ALA GLY HIS LEU LYS SEQRES 37 A 527 ASP ALA GLN ILE PHE ILE GLN LYS LYS ALA VAL LYS ASN SEQRES 38 A 527 PHE THR GLU VAL HIS PRO ASP TYR GLY SER HIS ILE GLN SEQRES 39 A 527 ALA LEU LEU ASP LYS TYR ASN ALA GLU LYS PRO LYS ASN SEQRES 40 A 527 ALA ILE HIS THR PHE VAL GLN SER GLY SER HIS LEU ALA SEQRES 41 A 527 ALA ARG GLU LYS ALA ASN LEU HET NDP A 601 48 HET HEM A 602 43 HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 NDP C21 H30 N7 O17 P3 FORMUL 3 HEM C34 H32 FE N4 O4 HELIX 1 AA1 ASP A 10 ALA A 20 1 11 HELIX 2 AA2 ASP A 54 ARG A 66 1 13 HELIX 3 AA3 ALA A 97 GLU A 101 5 5 HELIX 4 AA4 ASP A 157 ILE A 159 5 3 HELIX 5 AA5 LEU A 160 LYS A 169 1 10 HELIX 6 AA6 ASP A 178 ARG A 189 1 12 HELIX 7 AA7 SER A 192 SER A 201 1 10 HELIX 8 AA8 ASP A 202 ILE A 205 5 4 HELIX 9 AA9 GLY A 208 MET A 212 5 5 HELIX 10 AB1 SER A 246 ASP A 257 1 12 HELIX 11 AB2 ASP A 259 THR A 271 1 13 HELIX 12 AB3 THR A 285 PHE A 292 1 8 HELIX 13 AB4 ASN A 324 VAL A 329 1 6 HELIX 14 AB5 ASP A 348 LEU A 366 1 19 HELIX 15 AB6 ASN A 369 CYS A 377 5 9 HELIX 16 AB7 GLN A 415 LEU A 419 5 5 HELIX 17 AB8 VAL A 440 VAL A 450 1 11 HELIX 18 AB9 ASN A 452 LYS A 468 1 17 HELIX 19 AC1 GLN A 471 HIS A 486 1 16 HELIX 20 AC2 HIS A 486 LYS A 504 1 19 SHEET 1 AA111 ILE A 343 ALA A 345 0 SHEET 2 AA111 PHE A 220 VAL A 223 -1 N LYS A 221 O GLU A 344 SHEET 3 AA111 ALA A 229 THR A 238 -1 O VAL A 230 N LEU A 222 SHEET 4 AA111 SER A 276 MET A 284 -1 O TYR A 280 N HIS A 235 SHEET 5 AA111 ILE A 311 ARG A 320 -1 O ILE A 311 N ILE A 281 SHEET 6 AA111 GLY A 78 VAL A 87 -1 N PHE A 82 O ARG A 320 SHEET 7 AA111 LYS A 106 SER A 114 -1 O PHE A 113 N ALA A 79 SHEET 8 AA111 GLY A 131 THR A 138 -1 O LYS A 135 N ALA A 110 SHEET 9 AA111 GLY A 141 ASN A 148 -1 O GLY A 147 N PHE A 132 SHEET 10 AA111 GLY A 214 TYR A 215 -1 O TYR A 215 N ASN A 148 SHEET 11 AA111 ALA A 229 THR A 238 -1 O TYR A 236 N GLY A 214 LINK OH TYR A 358 FE HEM A 602 1555 1555 1.92 CISPEP 1 TYR A 405 PRO A 406 0 -2.34 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 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 -1.000000 0.000000 0.000000 211.32800 MTRIX2 2 0.000000 -1.000000 0.000000 211.32800 MTRIX3 2 0.000000 0.000000 1.000000 0.00000 MTRIX1 3 1.000000 0.000000 0.000000 0.00000 MTRIX2 3 0.000000 -1.000000 0.000000 211.32800 MTRIX3 3 0.000000 0.000000 -1.000000 211.32800 MTRIX1 4 -1.000000 0.000000 0.000000 211.32800 MTRIX2 4 0.000000 1.000000 0.000000 0.00000 MTRIX3 4 0.000000 0.000000 -1.000000 211.32800