HEADER OXIDOREDUCTASE 31-DEC-20 7L8Q TITLE CRYSTAL STRUCTURE OF HUMAN GPX4-U46C WITH OXIDIZED CYS-46 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; COMPND 8 OTHER_DETAILS: CYS-46 IS OXIDIZED, SO I NAMED IT SFO. 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 ALPHA-BETA PROTEIN, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR F.FOROUHAR,H.LIU,T.SEIBT,R.SANETO,K.WIGBY,J.FRIEDMAN,X.XIA, AUTHOR 2 M.S.SHCHEPINOV,S.RAMESH,M.CONRAD,B.R.STOCKWELL REVDAT 3 15-NOV-23 7L8Q 1 REMARK REVDAT 2 18-OCT-23 7L8Q 1 REMARK REVDAT 1 29-DEC-21 7L8Q 0 JRNL AUTH H.LIU,F.FOROUHAR,T.SEIBT,R.SANETO,K.WIGBY,J.FRIEDMAN,X.XIA, JRNL AUTH 2 M.S.SHCHEPINOV,S.RAMESH,M.CONRAD,B.R.STOCKWELL JRNL TITL PATIENT-DERIVED VARIANT OF GPX4 REVEALS THE STRUCTURAL BASIS JRNL TITL 2 FOR ITS CATALYTIC ACTIVITY AND DEGRADATION MECHANISM JRNL REF NAT.CHEM.BIOL. 2021 JRNL REFN ESSN 1552-4469 REMARK 2 REMARK 2 RESOLUTION. 1.48 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) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.440 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 23263 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.080 REMARK 3 FREE R VALUE TEST SET COUNT : 2346 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 34.5200 - 3.8000 0.99 1260 167 0.1309 0.1570 REMARK 3 2 3.8000 - 3.0200 0.99 1228 156 0.1262 0.1476 REMARK 3 3 3.0200 - 2.6400 1.00 1268 146 0.1609 0.1852 REMARK 3 4 2.6400 - 2.4000 0.98 1252 119 0.1526 0.1838 REMARK 3 5 2.4000 - 2.2300 0.98 1240 124 0.1482 0.1785 REMARK 3 6 2.2300 - 2.0900 0.99 1275 134 0.1488 0.1723 REMARK 3 7 2.0900 - 1.9900 0.99 1242 141 0.1537 0.1937 REMARK 3 8 1.9900 - 1.9000 0.99 1235 139 0.1504 0.1753 REMARK 3 9 1.9000 - 1.8300 0.99 1236 153 0.1461 0.1843 REMARK 3 10 1.8300 - 1.7700 0.97 1240 122 0.1576 0.1887 REMARK 3 11 1.7700 - 1.7100 0.96 1222 118 0.1504 0.2157 REMARK 3 12 1.7100 - 1.6600 0.98 1242 131 0.1573 0.1976 REMARK 3 13 1.6600 - 1.6200 0.98 1213 135 0.1667 0.2132 REMARK 3 14 1.6200 - 1.5800 0.96 1219 147 0.1988 0.2125 REMARK 3 15 1.5800 - 1.5400 0.96 1205 131 0.2563 0.2782 REMARK 3 16 1.5400 - 1.5100 0.95 1204 140 0.3291 0.3471 REMARK 3 17 1.5100 - 1.4800 0.93 1136 143 0.4290 0.4366 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.58 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): 0.1821 -0.3321 13.1804 REMARK 3 T TENSOR REMARK 3 T11: 0.0463 T22: 0.0502 REMARK 3 T33: 0.0423 T12: -0.0023 REMARK 3 T13: 0.0006 T23: -0.0134 REMARK 3 L TENSOR REMARK 3 L11: 1.6728 L22: 1.0127 REMARK 3 L33: 0.8746 L12: -0.0193 REMARK 3 L13: -0.1931 L23: -0.0348 REMARK 3 S TENSOR REMARK 3 S11: 0.0196 S12: 0.0844 S13: -0.0188 REMARK 3 S21: 0.0127 S22: 0.0093 S23: 0.0100 REMARK 3 S31: -0.0044 S32: -0.0002 S33: 0.1037 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 7L8Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1000253892. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 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-E 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 EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23698 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480 REMARK 200 RESOLUTION RANGE LOW (A) : 69.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 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: MOLREP REMARK 200 STARTING MODEL: 7L8K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 25.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M POTASSIUM THIOCYANATE, 0.1 M REMARK 280 SODIUM ACETATE, AND 20% (W/V) PEG 8000, PH 5, MICROBATCH, REMARK 280 TEMPERATURE 293K 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 34.51750 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 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 -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 DBREF 7L8Q A 3 170 UNP P36969 GPX4_HUMAN 30 197 SEQADV 7L8Q MET A -21 UNP P36969 INITIATING METHIONINE SEQADV 7L8Q GLY A -20 UNP P36969 EXPRESSION TAG SEQADV 7L8Q SER A -19 UNP P36969 EXPRESSION TAG SEQADV 7L8Q SER A -18 UNP P36969 EXPRESSION TAG SEQADV 7L8Q HIS A -17 UNP P36969 EXPRESSION TAG SEQADV 7L8Q HIS A -16 UNP P36969 EXPRESSION TAG SEQADV 7L8Q HIS A -15 UNP P36969 EXPRESSION TAG SEQADV 7L8Q HIS A -14 UNP P36969 EXPRESSION TAG SEQADV 7L8Q HIS A -13 UNP P36969 EXPRESSION TAG SEQADV 7L8Q HIS A -12 UNP P36969 EXPRESSION TAG SEQADV 7L8Q SER A -11 UNP P36969 EXPRESSION TAG SEQADV 7L8Q SER A -10 UNP P36969 EXPRESSION TAG SEQADV 7L8Q GLY A -9 UNP P36969 EXPRESSION TAG SEQADV 7L8Q LEU A -8 UNP P36969 EXPRESSION TAG SEQADV 7L8Q VAL A -7 UNP P36969 EXPRESSION TAG SEQADV 7L8Q PRO A -6 UNP P36969 EXPRESSION TAG SEQADV 7L8Q ARG A -5 UNP P36969 EXPRESSION TAG SEQADV 7L8Q GLY A -4 UNP P36969 EXPRESSION TAG SEQADV 7L8Q SER A -3 UNP P36969 EXPRESSION TAG SEQADV 7L8Q HIS A -2 UNP P36969 EXPRESSION TAG SEQADV 7L8Q MET A -1 UNP P36969 EXPRESSION TAG SEQADV 7L8Q LEU A 0 UNP P36969 EXPRESSION TAG SEQADV 7L8Q GLU A 1 UNP P36969 EXPRESSION TAG SEQADV 7L8Q ALA A 2 UNP P36969 EXPRESSION TAG SEQADV 7L8Q OCS A 46 UNP P36969 SEC 73 ENGINEERED MUTATION 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 OCS 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 ARG TYR GLY PRO MET GLU GLU PRO LEU SEQRES 15 A 192 VAL ILE GLU LYS ASP LEU PRO HIS TYR PHE HET OCS A 46 9 HET ACT A 201 4 HET ACT A 202 4 HETNAM OCS CYSTEINESULFONIC ACID HETNAM ACT ACETATE ION FORMUL 1 OCS C3 H7 N O5 S FORMUL 2 ACT 2(C2 H3 O2 1-) FORMUL 4 HOH *212(H2 O) HELIX 1 AA1 ASP A 6 ALA A 11 5 6 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 LYS A 121 1 8 HELIX 7 AA7 GLU A 158 LEU A 166 5 9 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 THR A 40 O PHE A 73 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 VAL A 150 N LEU A 142 LINK C GLN A 45 N OCS A 46 1555 1555 1.33 LINK C OCS A 46 N GLY A 47 1555 1555 1.33 CRYST1 32.757 69.035 35.678 90.00 115.88 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 0.030528 0.000000 0.014812 0.00000 SCALE2 0.000000 0.014485 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031154 0.00000