HEADER OXIDOREDUCTASE 19-JUN-23 8JSC TITLE STRUCTURE OF THE FSP1 PROTEIN FROM HUMAN COMPND MOL_ID: 1; COMPND 2 MOLECULE: FERROPTOSIS SUPPRESSOR PROTEIN 1; COMPND 3 CHAIN: C; COMPND 4 SYNONYM: FSP1,APOPTOSIS-INDUCING FACTOR HOMOLOGOUS MITOCHONDRION- COMPND 5 ASSOCIATED INDUCER OF DEATH,AMID,P53-RESPONSIVE GENE 3 PROTEIN; COMPND 6 EC: 1.6.5.-; COMPND 7 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: AIFM2, AMID, PRG3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NADH-UBIQUINONE OXIDOREDUCTASE, OXIDOREDUCTASE (E.C.1.-.-.-), KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.T.ZHANG,D.JIA REVDAT 1 13-MAR-24 8JSC 0 JRNL AUTH S.ZHANG,S.GOU,Q.ZHANG,X.YONG,B.GAN,D.JIA JRNL TITL FSP1 OXIDIZES NADPH TO SUPPRESS FERROPTOSIS. JRNL REF CELL RES. V. 33 967 2023 JRNL REFN ISSN 1001-0602 JRNL PMID 37739993 JRNL DOI 10.1038/S41422-023-00879-Z REMARK 2 REMARK 2 RESOLUTION. 2.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 18340 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.480 REMARK 3 FREE R VALUE TEST SET COUNT : 825 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 3.9200 - 3.1100 0.99 2967 122 0.1691 0.1940 REMARK 3 2 3.1100 - 2.7200 1.00 2944 133 0.1841 0.2555 REMARK 3 3 2.7200 - 2.4700 0.99 2934 121 0.2040 0.2675 REMARK 3 4 2.4700 - 2.2900 0.99 2871 140 0.2108 0.2765 REMARK 3 5 2.2900 - 2.1600 0.98 2864 166 0.2356 0.2916 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.284 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.906 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.012 2941 REMARK 3 ANGLE : 1.282 3996 REMARK 3 CHIRALITY : 0.071 458 REMARK 3 PLANARITY : 0.007 499 REMARK 3 DIHEDRAL : 20.900 1088 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8JSC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 27-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1300038154. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-AUG-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : ADDREF REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18472 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.160 REMARK 200 RESOLUTION RANGE LOW (A) : 62.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX V1.13 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, AMMONIUM NITRATE., VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 19.56300 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 GLY C 2 REMARK 465 SER C 3 REMARK 465 GLN C 4 REMARK 465 VAL C 5 REMARK 465 SER C 6 REMARK 465 VAL C 7 REMARK 465 GLU C 8 REMARK 465 SER C 9 REMARK 465 GLY C 10 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 C 13 117.33 -169.51 REMARK 500 HIS C 48 74.52 -69.88 REMARK 500 LYS C 74 -123.88 59.72 REMARK 500 PHE C 115 -78.75 -44.06 REMARK 500 ALA C 180 -169.34 63.71 REMARK 500 ARG C 290 51.55 -96.90 REMARK 500 PHE C 328 118.95 -163.09 REMARK 500 LYS C 355 -54.29 -122.54 REMARK 500 REMARK 500 REMARK: NULL DBREF 8JSC C 2 373 UNP Q9BRQ8 FSP1_HUMAN 2 373 SEQRES 1 C 372 GLY SER GLN VAL SER VAL GLU SER GLY ALA LEU HIS VAL SEQRES 2 C 372 VAL ILE VAL GLY GLY GLY PHE GLY GLY ILE ALA ALA ALA SEQRES 3 C 372 SER GLN LEU GLN ALA LEU ASN VAL PRO PHE MET LEU VAL SEQRES 4 C 372 ASP MET LYS ASP SER PHE HIS HIS ASN VAL ALA ALA LEU SEQRES 5 C 372 ARG ALA SER VAL GLU THR GLY PHE ALA LYS LYS THR PHE SEQRES 6 C 372 ILE SER TYR SER VAL THR PHE LYS ASP ASN PHE ARG GLN SEQRES 7 C 372 GLY LEU VAL VAL GLY ILE ASP LEU LYS ASN GLN MET VAL SEQRES 8 C 372 LEU LEU GLN GLY GLY GLU ALA LEU PRO PHE SER HIS LEU SEQRES 9 C 372 ILE LEU ALA THR GLY SER THR GLY PRO PHE PRO GLY LYS SEQRES 10 C 372 PHE ASN GLU VAL SER SER GLN GLN ALA ALA ILE GLN ALA SEQRES 11 C 372 TYR GLU ASP MET VAL ARG GLN VAL GLN ARG SER ARG PHE SEQRES 12 C 372 ILE VAL VAL VAL GLY GLY GLY SER ALA GLY VAL GLU MET SEQRES 13 C 372 ALA ALA GLU ILE LYS THR GLU TYR PRO GLU LYS GLU VAL SEQRES 14 C 372 THR LEU ILE HIS SER GLN VAL ALA LEU ALA ASP LYS GLU SEQRES 15 C 372 LEU LEU PRO SER VAL ARG GLN GLU VAL LYS GLU ILE LEU SEQRES 16 C 372 LEU ARG LYS GLY VAL GLN LEU LEU LEU SER GLU ARG VAL SEQRES 17 C 372 SER ASN LEU GLU GLU LEU PRO LEU ASN GLU TYR ARG GLU SEQRES 18 C 372 TYR ILE LYS VAL GLN THR ASP LYS GLY THR GLU VAL ALA SEQRES 19 C 372 THR ASN LEU VAL ILE LEU CYS THR GLY ILE LYS ILE ASN SEQRES 20 C 372 SER SER ALA TYR ARG LYS ALA PHE GLU SER ARG LEU ALA SEQRES 21 C 372 SER SER GLY ALA LEU ARG VAL ASN GLU HIS LEU GLN VAL SEQRES 22 C 372 GLU GLY HIS SER ASN VAL TYR ALA ILE GLY ASP CYS ALA SEQRES 23 C 372 ASP VAL ARG THR PRO LYS MET ALA TYR LEU ALA GLY LEU SEQRES 24 C 372 HIS ALA ASN ILE ALA VAL ALA ASN ILE VAL ASN SER VAL SEQRES 25 C 372 LYS GLN ARG PRO LEU GLN ALA TYR LYS PRO GLY ALA LEU SEQRES 26 C 372 THR PHE LEU LEU SER MET GLY ARG ASN ASP GLY VAL GLY SEQRES 27 C 372 GLN ILE SER GLY PHE TYR VAL GLY ARG LEU MET VAL ARG SEQRES 28 C 372 LEU THR LYS SER ARG ASP LEU PHE VAL SER THR SER TRP SEQRES 29 C 372 LYS THR MET ARG GLN SER PRO PRO HET 6FA C 401 54 HET NAP C 402 48 HETNAM 6FA 6-HYDROXY-FLAVIN-ADENINE DINUCLEOTIDE HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 6FA C27 H33 N9 O16 P2 FORMUL 3 NAP C21 H28 N7 O17 P3 FORMUL 4 HOH *152(H2 O) HELIX 1 AA1 GLY C 20 LEU C 33 1 14 HELIX 2 AA2 ALA C 51 SER C 56 1 6 HELIX 3 AA3 PHE C 61 LYS C 64 5 4 HELIX 4 AA4 TYR C 69 LYS C 74 1 6 HELIX 5 AA5 SER C 124 SER C 142 1 19 HELIX 6 AA6 GLY C 151 TYR C 165 1 15 HELIX 7 AA7 LEU C 185 GLY C 200 1 16 HELIX 8 AA8 ASN C 211 LEU C 215 5 5 HELIX 9 AA9 PHE C 256 LEU C 260 5 5 HELIX 10 AB1 GLY C 284 ALA C 287 5 4 HELIX 11 AB2 MET C 294 LYS C 314 1 21 HELIX 12 AB3 GLY C 347 LYS C 355 1 9 HELIX 13 AB4 PHE C 360 ARG C 369 1 10 SHEET 1 AA1 5 PHE C 77 GLN C 79 0 SHEET 2 AA1 5 PHE C 37 ASP C 41 1 N LEU C 39 O ARG C 78 SHEET 3 AA1 5 VAL C 14 VAL C 17 1 N ILE C 16 O MET C 38 SHEET 4 AA1 5 HIS C 104 LEU C 107 1 O ILE C 106 N VAL C 17 SHEET 5 AA1 5 VAL C 280 ALA C 282 1 O TYR C 281 N LEU C 107 SHEET 1 AA2 2 SER C 45 HIS C 47 0 SHEET 2 AA2 2 PHE C 66 SER C 68 -1 O ILE C 67 N PHE C 46 SHEET 1 AA3 3 VAL C 82 ASP C 86 0 SHEET 2 AA3 3 MET C 91 LEU C 94 -1 O MET C 91 N ASP C 86 SHEET 3 AA3 3 ALA C 99 PRO C 101 -1 O LEU C 100 N VAL C 92 SHEET 1 AA4 2 SER C 111 THR C 112 0 SHEET 2 AA4 2 LYS C 246 ILE C 247 -1 O LYS C 246 N THR C 112 SHEET 1 AA5 4 GLN C 202 LEU C 204 0 SHEET 2 AA5 4 GLU C 169 ILE C 173 1 N VAL C 170 O GLN C 202 SHEET 3 AA5 4 PHE C 144 VAL C 148 1 N VAL C 147 O THR C 171 SHEET 4 AA5 4 LEU C 238 LEU C 241 1 O ILE C 240 N VAL C 148 SHEET 1 AA6 2 ILE C 224 GLN C 227 0 SHEET 2 AA6 2 GLU C 233 THR C 236 -1 O VAL C 234 N VAL C 226 SHEET 1 AA7 3 PHE C 328 SER C 331 0 SHEET 2 AA7 3 GLY C 337 ILE C 341 -1 O VAL C 338 N LEU C 330 SHEET 3 AA7 3 PHE C 344 VAL C 346 -1 O PHE C 344 N ILE C 341 CRYST1 65.820 39.126 70.345 90.00 108.95 90.00 P 1 21 1 2 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 0.015193 0.000000 0.005217 0.00000 SCALE2 0.000000 0.025558 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015030 0.00000