HEADER MEMBRANE PROTEIN 12-OCT-23 8QTA TITLE CRYO-EM STRUCTURE OF STREPTOCOCCUS PNEUMONIAE NADPH OXIDASE F397A TITLE 2 MUTANT IN COMPLEX WITH NADPH COMPND MOL_ID: 1; COMPND 2 MOLECULE: FAD-BINDING FR-TYPE DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 1313; SOURCE 4 GENE: SPR0531; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS NADPH OXIDASE, ROS PRODUCING, FLAVOPROTEIN, HEME PROTEIN, MEMBRANE KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR V.R.A.DUBACH,P.SAN SEGUNDO-ACOSTA,B.J.MURPHY REVDAT 2 31-JUL-24 8QTA 1 JRNL REVDAT 1 24-JUL-24 8QTA 0 JRNL AUTH V.R.A.DUBACH,P.SAN SEGUNDO-ACOSTA,B.J.MURPHY JRNL TITL STRUCTURAL AND MECHANISTIC INSIGHTS INTO STREPTOCOCCUS JRNL TITL 2 PNEUMONIAE NADPH OXIDASE. JRNL REF NAT.STRUCT.MOL.BIOL. 2024 JRNL REFN ESSN 1545-9985 JRNL PMID 39039317 JRNL DOI 10.1038/S41594-024-01348-W REMARK 2 REMARK 2 RESOLUTION. 2.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : TOPAZ, CRYOLO, EPU, CTFFIND, UCSF REMARK 3 CHIMERAX, PHENIX, COOT, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : CROSS-CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : INITIAL MODEL WAS FIT USING CHIMERAX AND REMARK 3 REFINED WITH COOT AND PHENIX 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) : 2.640 REMARK 3 NUMBER OF PARTICLES : 546234 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: FINAL REFINEMENT WAS LOCAL REFINEMENT IN CRYOSPARC REMARK 3 4.1 WITH A MASK EXCLUDING THE DETERGENT MICELLE REMARK 4 REMARK 4 8QTA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1292133231. 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 : PROTEIN-SUBSTRATE COMPLEX OF REMARK 245 NADPH OXIDASE WITH NADPH REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 6.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL 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 : 45181 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 700.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2100.00 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) : 7000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 215000 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 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 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 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 HIS A 60 -73.53 66.01 REMARK 500 LEU A 116 50.09 -91.55 REMARK 500 ASN A 149 -4.17 68.21 REMARK 500 ASN A 197 -166.79 -129.51 REMARK 500 SER A 238 30.45 -98.82 REMARK 500 ASP A 272 -62.53 -94.50 REMARK 500 MET A 278 58.48 -95.52 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 504 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 69 NE2 REMARK 620 2 HEM A 504 NA 88.8 REMARK 620 3 HEM A 504 NB 91.4 89.8 REMARK 620 4 HEM A 504 NC 87.4 176.2 90.4 REMARK 620 5 HEM A 504 ND 91.8 90.3 176.8 89.7 REMARK 620 6 HIS A 129 NE2 174.8 92.5 83.6 91.3 93.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 503 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 83 NE2 REMARK 620 2 HEM A 503 NA 78.8 REMARK 620 3 HEM A 503 NB 84.5 86.7 REMARK 620 4 HEM A 503 NC 95.9 172.6 87.7 REMARK 620 5 HEM A 503 ND 91.5 94.2 175.6 91.0 REMARK 620 6 HIS A 142 NE2 164.4 85.7 95.3 99.7 89.0 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-18647 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF STREPTOCOCCUS PNEUMONIAE NADPH OXIDASE F397A REMARK 900 MUTANT IN COMPLEX WITH NADPH DBREF 8QTA A 2 400 UNP Q8CZ28 Q8CZ28_STRR6 2 400 SEQADV 8QTA ALA A 397 UNP Q8CZ28 PHE 397 ENGINEERED MUTATION SEQRES 1 A 399 GLU PHE SER MET LYS SER VAL LYS GLY LEU LEU PHE ILE SEQRES 2 A 399 ILE ALA SER PHE ILE LEU THR LEU LEU THR TRP MET ASN SEQRES 3 A 399 THR SER PRO GLN PHE MET ILE PRO GLY LEU ALA LEU THR SEQRES 4 A 399 SER LEU SER LEU THR PHE ILE LEU ALA THR ARG LEU PRO SEQRES 5 A 399 LEU LEU GLU SER TRP PHE HIS SER LEU GLU LYS VAL TYR SEQRES 6 A 399 THR VAL HIS LYS PHE THR ALA PHE LEU SER ILE ILE LEU SEQRES 7 A 399 LEU ILE PHE HIS ASN PHE SER MET GLY GLY LEU TRP GLY SEQRES 8 A 399 SER ARG LEU ALA ALA GLN PHE GLY ASN LEU ALA ILE TYR SEQRES 9 A 399 ILE PHE ALA SER ILE ILE LEU VAL ALA TYR LEU GLY LYS SEQRES 10 A 399 TYR ILE GLN TYR GLU ALA TRP ARG TRP ILE HIS ARG LEU SEQRES 11 A 399 VAL TYR LEU ALA TYR ILE LEU GLY LEU PHE HIS ILE TYR SEQRES 12 A 399 MET ILE MET GLY ASN ARG LEU LEU THR PHE ASN LEU LEU SEQRES 13 A 399 SER PHE LEU VAL GLY SER TYR ALA LEU LEU GLY LEU LEU SEQRES 14 A 399 ALA GLY PHE TYR ILE ILE PHE LEU TYR GLN LYS ILE SER SEQRES 15 A 399 PHE PRO TYR LEU GLY LYS ILE THR HIS LEU LYS ARG LEU SEQRES 16 A 399 ASN HIS ASP THR ARG GLU ILE GLN ILE HIS LEU SER ARG SEQRES 17 A 399 PRO PHE ASN TYR GLN SER GLY GLN PHE ALA PHE LEU LYS SEQRES 18 A 399 ILE PHE GLN GLU GLY PHE GLU SER ALA PRO HIS PRO PHE SEQRES 19 A 399 SER ILE SER GLY GLY HIS GLY GLN THR LEU TYR PHE THR SEQRES 20 A 399 VAL LYS THR SER GLY ASP HIS THR LYS ASN ILE TYR ASP SEQRES 21 A 399 ASN LEU GLN ALA GLY SER LYS VAL THR LEU ASP ARG ALA SEQRES 22 A 399 TYR GLY HIS MET ILE ILE GLU GLU GLY ARG GLU ASN GLN SEQRES 23 A 399 VAL TRP ILE ALA GLY GLY ILE GLY ILE THR PRO PHE ILE SEQRES 24 A 399 SER TYR ILE ARG GLU HIS PRO ILE LEU ASP LYS GLN VAL SEQRES 25 A 399 HIS PHE TYR TYR SER PHE ARG GLY ASP GLU ASN ALA VAL SEQRES 26 A 399 TYR LEU ASP LEU LEU ARG ASN TYR ALA GLN LYS ASN PRO SEQRES 27 A 399 ASN PHE GLU LEU HIS LEU ILE ASP SER THR LYS ASP GLY SEQRES 28 A 399 TYR LEU ASN PHE GLU GLN LYS GLU VAL PRO GLU HIS ALA SEQRES 29 A 399 THR VAL TYR MET CYS GLY PRO ILE SER MET MET LYS ALA SEQRES 30 A 399 LEU ALA LYS GLN ILE LYS LYS GLN ASN PRO LYS THR GLU SEQRES 31 A 399 LEU ILE TYR GLU GLY ALA LYS PHE LYS HET NDP A 501 48 HET FAD A 502 53 HET HEM A 503 43 HET HEM A 504 43 HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 NDP C21 H30 N7 O17 P3 FORMUL 3 FAD C27 H33 N9 O15 P2 FORMUL 4 HEM 2(C34 H32 FE N4 O4) FORMUL 6 HOH *27(H2 O) HELIX 1 AA1 SER A 4 LYS A 6 5 3 HELIX 2 AA2 SER A 7 SER A 29 1 23 HELIX 3 AA3 PHE A 32 LEU A 48 1 17 HELIX 4 AA4 LEU A 52 PHE A 59 1 8 HELIX 5 AA5 SER A 61 GLY A 88 1 28 HELIX 6 AA6 ARG A 94 LEU A 116 1 23 HELIX 7 AA7 GLN A 121 ARG A 130 1 10 HELIX 8 AA8 LEU A 131 MET A 147 1 17 HELIX 9 AA9 ASN A 155 LEU A 178 1 24 HELIX 10 AB1 LEU A 178 SER A 183 1 6 HELIX 11 AB2 HIS A 255 LEU A 263 1 9 HELIX 12 AB3 ILE A 296 HIS A 306 1 11 HELIX 13 AB4 GLY A 321 ALA A 325 5 5 HELIX 14 AB5 TYR A 327 ASN A 338 1 12 HELIX 15 AB6 PRO A 372 ASN A 387 1 16 SHEET 1 AA1 6 HIS A 233 SER A 236 0 SHEET 2 AA1 6 PHE A 218 PHE A 224 -1 N LEU A 221 O HIS A 233 SHEET 3 AA1 6 LYS A 268 LEU A 271 -1 O LYS A 268 N PHE A 224 SHEET 4 AA1 6 TYR A 186 ASN A 197 -1 N GLY A 188 O VAL A 269 SHEET 5 AA1 6 THR A 200 PHE A 211 -1 O GLU A 202 N LYS A 194 SHEET 6 AA1 6 GLY A 242 LYS A 250 -1 O PHE A 247 N ILE A 203 SHEET 1 AA2 5 PHE A 341 ASP A 347 0 SHEET 2 AA2 5 GLN A 312 PHE A 319 1 N PHE A 315 O GLU A 342 SHEET 3 AA2 5 ASN A 286 GLY A 292 1 N TRP A 289 O HIS A 314 SHEET 4 AA2 5 ALA A 365 CYS A 370 1 O TYR A 368 N VAL A 288 SHEET 5 AA2 5 GLU A 391 GLU A 395 1 O GLU A 391 N VAL A 367 LINK NE2 HIS A 69 FE HEM A 504 1555 1555 2.18 LINK NE2 HIS A 83 FE HEM A 503 1555 1555 2.14 LINK NE2 HIS A 129 FE HEM A 504 1555 1555 2.21 LINK NE2 HIS A 142 FE HEM A 503 1555 1555 2.16 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