HEADER OXIDOREDUCTASE 18-AUG-23 8Q8J TITLE CRYSTAL STRUCTURE OF HUMAN GPX4-R152H COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTATHIONE PEROXIDASE; COMPND 3 CHAIN: A; COMPND 4 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: GPX4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS REDOX, FERROPTOSIS, GPX4, MEMBRANE ASSOCIATED, METABOLISM, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR V.NAPOLITANO,A.MOURAO,M.KOLONKO,M.J.BOSTOCK,M.SATTLER,M.CONRAD, AUTHOR 2 G.POPOWICZ REVDAT 1 28-AUG-24 8Q8J 0 JRNL AUTH S.M.LORENZ,A.WAHIDA,D.EMLER,M.BOSTOCK,T.SEIBT,A.MOURAO, JRNL AUTH 2 D.TRUMBACH,F.RIZZOLLO,V.NAPOLITANO,M.KOLONKO-ADAMSKA, JRNL AUTH 3 J.SOMMER,M.S.WOO,N.ROTHAMMER,S.GAUSSMAN,F.ALVES,E.BURKLE, JRNL AUTH 4 J.WANNINGER,K.M.BOXLEITNER,M.STADLER,S.DOLL,E.MISHIMA, JRNL AUTH 5 T.NAKAMURA,A.MAIDA,D.HASS,A.ESCAMILLA-AYALA,L.P.PUENTES, JRNL AUTH 6 J.LENBERG,J.FRIEDMAN,C.SCALE,B.PRONETH,L.HENKELMANN, JRNL AUTH 7 M.ALDROVANDI,P.AGOSTINIS,A.ZIMPRICH,D.VOGT-WEISENHORN, JRNL AUTH 8 S.HOLTER-KOCH,J.LEWERENZ,P.STEINACKER,A.J.GARCIA-SAEZ, JRNL AUTH 9 W.WURST,A.TIETZE,M.MANN,G.G.WESTMEYER,M.A.FRIESE,S.K.RAMESH, JRNL AUTH10 K.WIGBY,M.SATTLER,I.INGOLD,S.AYTON,A.K.JAYAVELU,G.POPOWICZ, JRNL AUTH11 M.CONRAD JRNL TITL CRYSTAL STRUCTURE OF HUMAN GPX4-R152H JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.890 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.0 REMARK 3 NUMBER OF REFLECTIONS : 8680 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 422 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 39.5900 - 2.8800 0.79 2688 135 0.1923 0.2085 REMARK 3 2 2.8800 - 2.2900 0.85 2732 151 0.2706 0.3114 REMARK 3 3 2.2900 - 2.0000 0.88 2838 136 0.2701 0.3085 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.040 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 NULL REMARK 3 ANGLE : 0.887 NULL REMARK 3 CHIRALITY : 0.059 193 REMARK 3 PLANARITY : 0.006 253 REMARK 3 DIHEDRAL : 6.339 189 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESSEQ 6:170) REMARK 3 ORIGIN FOR THE GROUP (A): 9.1288 2.0252 10.7485 REMARK 3 T TENSOR REMARK 3 T11: 0.2517 T22: 0.2518 REMARK 3 T33: 0.2250 T12: 0.0261 REMARK 3 T13: -0.0532 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 4.4597 L22: 3.4166 REMARK 3 L33: 3.0426 L12: 0.4217 REMARK 3 L13: 0.3587 L23: 0.4039 REMARK 3 S TENSOR REMARK 3 S11: -0.0097 S12: -0.0956 S13: -0.0054 REMARK 3 S21: -0.0364 S22: 0.0062 S23: 0.0030 REMARK 3 S31: -0.0561 S32: -0.0457 S33: 0.0221 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 8Q8J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1292132836. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-AUG-21 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 : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8691 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 45.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.2 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 8.90 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% W/V PEG MONOMETHYLETHER 5000 200 REMARK 280 MM LITHIUM SULPHATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 19.43550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.47700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.52400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.47700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.43550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.52400 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 125 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 203 O HOH A 228 2.09 REMARK 500 OE1 GLU A 65 O HOH A 201 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 ASN A 132 19.43 59.73 REMARK 500 PHE A 138 33.03 73.65 REMARK 500 REMARK 500 REMARK: NULL DBREF 8Q8J A 14 168 UNP K7ERP4 K7ERP4_HUMAN 1 155 SEQADV 8Q8J ASP A 6 UNP K7ERP4 EXPRESSION TAG SEQADV 8Q8J ASP A 7 UNP K7ERP4 EXPRESSION TAG SEQADV 8Q8J TRP A 8 UNP K7ERP4 EXPRESSION TAG SEQADV 8Q8J ARG A 9 UNP K7ERP4 EXPRESSION TAG SEQADV 8Q8J CYS A 10 UNP K7ERP4 EXPRESSION TAG SEQADV 8Q8J ALA A 11 UNP K7ERP4 EXPRESSION TAG SEQADV 8Q8J ARG A 12 UNP K7ERP4 EXPRESSION TAG SEQADV 8Q8J SER A 13 UNP K7ERP4 EXPRESSION TAG SEQADV 8Q8J HIS A 152 UNP K7ERP4 ARG 139 ENGINEERED MUTATION SEQADV 8Q8J TYR A 169 UNP K7ERP4 EXPRESSION TAG SEQADV 8Q8J PHE A 170 UNP K7ERP4 EXPRESSION TAG SEQRES 1 A 165 ASP ASP TRP ARG CYS ALA ARG SER MET HIS GLU PHE SER SEQRES 2 A 165 ALA LYS ASP ILE ASP GLY HIS MET VAL ASN LEU ASP LYS SEQRES 3 A 165 TYR ARG GLY PHE VAL CYS ILE VAL THR ASN VAL ALA SER SEQRES 4 A 165 GLN CYS GLY LYS THR GLU VAL ASN TYR THR GLN LEU VAL SEQRES 5 A 165 ASP LEU HIS ALA ARG TYR ALA GLU CYS GLY LEU ARG ILE SEQRES 6 A 165 LEU ALA PHE PRO CYS ASN GLN PHE GLY LYS GLN GLU PRO SEQRES 7 A 165 GLY SER ASN GLU GLU ILE LYS GLU PHE ALA ALA GLY TYR SEQRES 8 A 165 ASN VAL LYS PHE ASP MET PHE SER LYS ILE CYS VAL ASN SEQRES 9 A 165 GLY ASP ASP ALA HIS PRO LEU TRP LYS TRP MET LYS ILE SEQRES 10 A 165 GLN PRO LYS GLY LYS GLY ILE LEU GLY ASN ALA ILE LYS SEQRES 11 A 165 TRP ASN PHE THR LYS PHE LEU ILE ASP LYS ASN GLY CYS SEQRES 12 A 165 VAL VAL LYS HIS TYR GLY PRO MET GLU GLU PRO LEU VAL SEQRES 13 A 165 ILE GLU LYS ASP LEU PRO HIS TYR PHE FORMUL 2 HOH *47(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 GLY A 95 1 11 HELIX 6 AA6 HIS A 114 LYS A 121 1 8 HELIX 7 AA7 ILE A 129 ALA A 133 5 5 HELIX 8 AA8 GLU A 158 GLU A 163 5 6 HELIX 9 AA9 ASP A 165 TYR A 169 5 5 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 VAL A 36 O ARG A 69 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 CISPEP 1 GLN A 123 PRO A 124 0 -8.47 CRYST1 38.871 45.048 82.954 90.00 90.00 90.00 P 21 21 21 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 0.025726 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022199 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012055 0.00000