HEADER OXIDOREDUCTASE 28-FEB-22 7U4J TITLE CRYSTAL STRUCTURE OF HUMAN GPX4-U46C-R152H IN COMPLEX WITH TMT10 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPID HYDROPEROXIDE GLUTATHIONE PEROXIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PHGPX,GLUTATHIONE PEROXIDASE 4,GSHPX-4; COMPND 5 EC: 1.11.1.12; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: GPX4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GPX4, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR F.FOROUHAR,H.LIU,A.J.LIN,Q.WANG,V.POLYCHRONIDOU,R.K.SONI,X.XIA, AUTHOR 2 B.R.STOCKWELL REVDAT 4 25-OCT-23 7U4J 1 REMARK REVDAT 3 28-DEC-22 7U4J 1 JRNL REVDAT 2 14-DEC-22 7U4J 1 JRNL REVDAT 1 07-DEC-22 7U4J 0 JRNL AUTH H.LIU,F.FOROUHAR,A.J.LIN,Q.WANG,V.POLYCHRONIDOU,R.K.SONI, JRNL AUTH 2 X.XIA,B.R.STOCKWELL JRNL TITL SMALL-MOLECULE ALLOSTERIC INHIBITORS OF GPX4. JRNL REF CELL CHEM BIOL V. 29 1680 2022 JRNL REFN ESSN 2451-9456 JRNL PMID 36423641 JRNL DOI 10.1016/J.CHEMBIOL.2022.11.003 REMARK 2 REMARK 2 RESOLUTION. 1.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 17486 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.680 REMARK 3 FREE R VALUE TEST SET COUNT : 1692 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 41.3600 - 4.1400 0.98 1376 142 0.1728 0.1883 REMARK 3 2 4.1400 - 3.2900 0.99 1322 153 0.1501 0.1918 REMARK 3 3 3.2900 - 2.8700 1.00 1345 140 0.1644 0.1891 REMARK 3 4 2.8700 - 2.6100 0.99 1314 143 0.1812 0.1967 REMARK 3 5 2.6100 - 2.4200 0.99 1311 141 0.1655 0.2112 REMARK 3 6 2.4200 - 2.2800 0.99 1333 138 0.1562 0.1960 REMARK 3 7 2.2800 - 2.1700 0.99 1292 149 0.1628 0.2089 REMARK 3 8 2.1700 - 2.0700 0.98 1316 140 0.1642 0.2220 REMARK 3 9 2.0700 - 1.9900 0.98 1308 121 0.1828 0.2243 REMARK 3 10 1.9900 - 1.9200 1.00 1311 131 0.1968 0.2452 REMARK 3 11 1.9200 - 1.8600 0.96 1288 136 0.2078 0.2799 REMARK 3 12 1.8600 - 1.8100 0.98 1278 158 0.2405 0.2773 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.25 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 19.1127 -0.3643 5.6072 REMARK 3 T TENSOR REMARK 3 T11: 0.1064 T22: 0.0662 REMARK 3 T33: 0.0721 T12: -0.0025 REMARK 3 T13: -0.0041 T23: -0.0024 REMARK 3 L TENSOR REMARK 3 L11: 0.6441 L22: 1.2627 REMARK 3 L33: 0.4394 L12: 0.2911 REMARK 3 L13: -0.0058 L23: 0.1135 REMARK 3 S TENSOR REMARK 3 S11: 0.0188 S12: 0.0084 S13: 0.0558 REMARK 3 S21: 0.0833 S22: -0.0678 S23: 0.3139 REMARK 3 S31: -0.0339 S32: 0.0254 S33: -0.1634 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 7U4J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1000263515. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23632 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.620 REMARK 200 RESOLUTION RANGE LOW (A) : 41.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.26500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 38.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 1.71100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 7L8L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM THIOCYANATE AND 20% REMARK 280 (W/V) PEG 3350, PH 7, MICROBATCH, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 64.04750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.28400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 64.04750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.28400 REMARK 290 SMTRY3 4 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 454 LIES ON A SPECIAL POSITION. 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 -21 REMARK 465 GLY A -20 REMARK 465 SER A -19 REMARK 465 SER A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 SER A -11 REMARK 465 SER A -10 REMARK 465 GLY A -9 REMARK 465 LEU A -8 REMARK 465 VAL A -7 REMARK 465 PRO A -6 REMARK 465 ARG A -5 REMARK 465 GLY A -4 REMARK 465 SER A -3 REMARK 465 HIS A -2 REMARK 465 MET A -1 REMARK 465 LEU A 0 REMARK 465 GLU A 1 REMARK 465 ALA A 2 REMARK 465 ALA A 3 REMARK 465 SER A 4 REMARK 465 ARG A 5 REMARK 465 ASP A 6 REMARK 465 LYS A 125 REMARK 465 GLY A 126 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 458 DISTANCE = 6.54 ANGSTROMS REMARK 525 HOH A 459 DISTANCE = 7.05 ANGSTROMS DBREF 7U4J A 3 170 UNP P36969 GPX4_HUMAN 30 197 SEQADV 7U4J MET A -21 UNP P36969 INITIATING METHIONINE SEQADV 7U4J GLY A -20 UNP P36969 EXPRESSION TAG SEQADV 7U4J SER A -19 UNP P36969 EXPRESSION TAG SEQADV 7U4J SER A -18 UNP P36969 EXPRESSION TAG SEQADV 7U4J HIS A -17 UNP P36969 EXPRESSION TAG SEQADV 7U4J HIS A -16 UNP P36969 EXPRESSION TAG SEQADV 7U4J HIS A -15 UNP P36969 EXPRESSION TAG SEQADV 7U4J HIS A -14 UNP P36969 EXPRESSION TAG SEQADV 7U4J HIS A -13 UNP P36969 EXPRESSION TAG SEQADV 7U4J HIS A -12 UNP P36969 EXPRESSION TAG SEQADV 7U4J SER A -11 UNP P36969 EXPRESSION TAG SEQADV 7U4J SER A -10 UNP P36969 EXPRESSION TAG SEQADV 7U4J GLY A -9 UNP P36969 EXPRESSION TAG SEQADV 7U4J LEU A -8 UNP P36969 EXPRESSION TAG SEQADV 7U4J VAL A -7 UNP P36969 EXPRESSION TAG SEQADV 7U4J PRO A -6 UNP P36969 EXPRESSION TAG SEQADV 7U4J ARG A -5 UNP P36969 EXPRESSION TAG SEQADV 7U4J GLY A -4 UNP P36969 EXPRESSION TAG SEQADV 7U4J SER A -3 UNP P36969 EXPRESSION TAG SEQADV 7U4J HIS A -2 UNP P36969 EXPRESSION TAG SEQADV 7U4J MET A -1 UNP P36969 EXPRESSION TAG SEQADV 7U4J LEU A 0 UNP P36969 EXPRESSION TAG SEQADV 7U4J GLU A 1 UNP P36969 EXPRESSION TAG SEQADV 7U4J ALA A 2 UNP P36969 EXPRESSION TAG SEQADV 7U4J CYS A 46 UNP P36969 SEC 73 CONFLICT SEQADV 7U4J HIS A 152 UNP P36969 ARG 179 CONFLICT SEQRES 1 A 192 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 192 LEU VAL PRO ARG GLY SER HIS MET LEU GLU ALA ALA SER SEQRES 3 A 192 ARG ASP ASP TRP ARG CYS ALA ARG SER MET HIS GLU PHE SEQRES 4 A 192 SER ALA LYS ASP ILE ASP GLY HIS MET VAL ASN LEU ASP SEQRES 5 A 192 LYS TYR ARG GLY PHE VAL CYS ILE VAL THR ASN VAL ALA SEQRES 6 A 192 SER GLN CYS GLY LYS THR GLU VAL ASN TYR THR GLN LEU SEQRES 7 A 192 VAL ASP LEU HIS ALA ARG TYR ALA GLU CYS GLY LEU ARG SEQRES 8 A 192 ILE LEU ALA PHE PRO CYS ASN GLN PHE GLY LYS GLN GLU SEQRES 9 A 192 PRO GLY SER ASN GLU GLU ILE LYS GLU PHE ALA ALA GLY SEQRES 10 A 192 TYR ASN VAL LYS PHE ASP MET PHE SER LYS ILE CYS VAL SEQRES 11 A 192 ASN GLY ASP ASP ALA HIS PRO LEU TRP LYS TRP MET LYS SEQRES 12 A 192 ILE GLN PRO LYS GLY LYS GLY ILE LEU GLY ASN ALA ILE SEQRES 13 A 192 LYS TRP ASN PHE THR LYS PHE LEU ILE ASP LYS ASN GLY SEQRES 14 A 192 CYS VAL VAL LYS HIS TYR GLY PRO MET GLU GLU PRO LEU SEQRES 15 A 192 VAL ILE GLU LYS ASP LEU PRO HIS TYR PHE HET 8NB A 201 13 HET SCN A 202 3 HETNAM 8NB ~{N}-(3-CHLORANYL-4-METHOXY-PHENYL)ETHANAMIDE HETNAM SCN THIOCYANATE ION FORMUL 2 8NB C9 H10 CL N O2 FORMUL 3 SCN C N S 1- FORMUL 4 HOH *159(H2 O) HELIX 1 AA1 ASP A 7 ALA A 11 5 5 HELIX 2 AA2 SER A 13 GLU A 16 5 4 HELIX 3 AA3 ASP A 30 ARG A 33 5 4 HELIX 4 AA4 LYS A 48 ALA A 64 1 17 HELIX 5 AA5 SER A 85 TYR A 96 1 12 HELIX 6 AA6 HIS A 114 ILE A 122 1 9 HELIX 7 AA7 GLU A 158 TYR A 169 5 12 SHEET 1 AA1 2 SER A 18 LYS A 20 0 SHEET 2 AA1 2 MET A 26 ASN A 28 -1 O VAL A 27 N ALA A 19 SHEET 1 AA2 5 ASP A 101 MET A 102 0 SHEET 2 AA2 5 LEU A 68 PRO A 74 1 N ALA A 72 O ASP A 101 SHEET 3 AA2 5 VAL A 36 VAL A 42 1 N ILE A 38 O LEU A 71 SHEET 4 AA2 5 LYS A 140 ILE A 143 -1 O ILE A 143 N CYS A 37 SHEET 5 AA2 5 VAL A 149 TYR A 153 -1 O TYR A 153 N LYS A 140 LINK SG CYS A 66 C9 8NB A 201 1555 1555 1.83 CRYST1 128.095 36.568 42.180 90.00 101.30 90.00 C 1 2 1 4 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 0.007807 0.000000 0.001561 0.00000 SCALE2 0.000000 0.027346 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024177 0.00000