HEADER TRANSCRIPTION 10-FEB-20 6LXB TITLE X-RAY STRUCTURE OF HUMAN PPARALPHA LIGAND BINDING DOMAIN-SAROGLITAZAR TITLE 2 CO-CRYSTALS OBTAINED BY SOAKING COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR ALPHA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS NUCLEAR RECEPTOR, PROTEIN-LIGAND COMPLEX, PPAR, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR S.KAMATA,A.HONDA,R.ISHIKAWA,M.AKAHANE,T.OYAMA,I.ISHII REVDAT 3 29-NOV-23 6LXB 1 REMARK REVDAT 2 02-DEC-20 6LXB 1 JRNL REVDAT 1 11-NOV-20 6LXB 0 JRNL AUTH S.KAMATA,T.OYAMA,K.SAITO,A.HONDA,Y.YAMAMOTO,K.SUDA, JRNL AUTH 2 R.ISHIKAWA,T.ITOH,Y.WATANABE,T.SHIBATA,K.UCHIDA,M.SUEMATSU, JRNL AUTH 3 I.ISHII JRNL TITL PPAR ALPHA LIGAND-BINDING DOMAIN STRUCTURES WITH ENDOGENOUS JRNL TITL 2 FATTY ACIDS AND FIBRATES. JRNL REF ISCIENCE V. 23 01727 2020 JRNL REFN ESSN 2589-0042 JRNL PMID 33205029 JRNL DOI 10.1016/J.ISCI.2020.101727 REMARK 2 REMARK 2 RESOLUTION. 2.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1-2575-000 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.930 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 11683 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1142 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 35.3620 - 4.7169 0.98 2652 136 0.1730 0.1976 REMARK 3 2 4.7169 - 3.7453 0.97 2593 149 0.1612 0.1753 REMARK 3 3 3.7453 - 3.2723 0.97 2652 152 0.2039 0.2567 REMARK 3 4 3.2723 - 2.9732 0.96 2538 174 0.2456 0.3079 REMARK 3 5 2.9732 - 2.7602 0.97 2638 141 0.2411 0.2851 REMARK 3 6 2.7602 - 2.5975 0.96 2612 125 0.2474 0.2851 REMARK 3 7 2.5975 - 2.4675 0.96 2593 135 0.2542 0.2910 REMARK 3 8 2.4675 - 2.3601 0.93 2539 130 0.2658 0.3296 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.560 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.23 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 : 0.003 2113 REMARK 3 ANGLE : 0.545 2847 REMARK 3 CHIRALITY : 0.037 325 REMARK 3 PLANARITY : 0.004 359 REMARK 3 DIHEDRAL : 15.027 1282 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: SF FILE CONTAINS FRIEDEL PAIRS UNDER REMARK 3 I/F_MINUS AND I/F_PLUS COLUMNS. REMARK 4 REMARK 4 6LXB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1300015619. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-19 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11702 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.360 REMARK 200 RESOLUTION RANGE LOW (A) : 42.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.34200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.7.16 REMARK 200 STARTING MODEL: 3VI8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS(PH 6.5), 25 %(W/V) REMARK 280 PEG3350, VAPOR DIFFUSION, TEMPERATURE 277K 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 31.15850 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 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 GLY A 196 REMARK 465 SER A 197 REMARK 465 HIS A 198 REMARK 465 MET A 199 REMARK 465 LYS A 232 REMARK 465 ALA A 233 REMARK 465 SER A 234 REMARK 465 ASN A 235 REMARK 465 ASN A 236 REMARK 465 LEU A 258 REMARK 465 VAL A 259 REMARK 465 ALA A 260 REMARK 465 ASN A 261 REMARK 465 GLY A 262 REMARK 465 ILE A 263 REMARK 465 GLN A 264 REMARK 465 ASN A 265 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 SER A 230 -84.64 -78.87 REMARK 500 GLU A 267 130.52 146.80 REMARK 500 CYS A 384 33.47 -92.22 REMARK 500 THR A 450 -159.46 -83.28 REMARK 500 GLU A 451 76.54 40.32 REMARK 500 MET A 467 -94.80 -77.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EWR A 501 DBREF 6LXB A 200 468 UNP Q07869 PPARA_HUMAN 200 468 SEQADV 6LXB GLY A 196 UNP Q07869 EXPRESSION TAG SEQADV 6LXB SER A 197 UNP Q07869 EXPRESSION TAG SEQADV 6LXB HIS A 198 UNP Q07869 EXPRESSION TAG SEQADV 6LXB MET A 199 UNP Q07869 EXPRESSION TAG SEQRES 1 A 273 GLY SER HIS MET THR ALA ASP LEU LYS SER LEU ALA LYS SEQRES 2 A 273 ARG ILE TYR GLU ALA TYR LEU LYS ASN PHE ASN MET ASN SEQRES 3 A 273 LYS VAL LYS ALA ARG VAL ILE LEU SER GLY LYS ALA SER SEQRES 4 A 273 ASN ASN PRO PRO PHE VAL ILE HIS ASP MET GLU THR LEU SEQRES 5 A 273 CYS MET ALA GLU LYS THR LEU VAL ALA LYS LEU VAL ALA SEQRES 6 A 273 ASN GLY ILE GLN ASN LYS GLU ALA GLU VAL ARG ILE PHE SEQRES 7 A 273 HIS CYS CYS GLN CYS THR SER VAL GLU THR VAL THR GLU SEQRES 8 A 273 LEU THR GLU PHE ALA LYS ALA ILE PRO GLY PHE ALA ASN SEQRES 9 A 273 LEU ASP LEU ASN ASP GLN VAL THR LEU LEU LYS TYR GLY SEQRES 10 A 273 VAL TYR GLU ALA ILE PHE ALA MET LEU SER SER VAL MET SEQRES 11 A 273 ASN LYS ASP GLY MET LEU VAL ALA TYR GLY ASN GLY PHE SEQRES 12 A 273 ILE THR ARG GLU PHE LEU LYS SER LEU ARG LYS PRO PHE SEQRES 13 A 273 CYS ASP ILE MET GLU PRO LYS PHE ASP PHE ALA MET LYS SEQRES 14 A 273 PHE ASN ALA LEU GLU LEU ASP ASP SER ASP ILE SER LEU SEQRES 15 A 273 PHE VAL ALA ALA ILE ILE CYS CYS GLY ASP ARG PRO GLY SEQRES 16 A 273 LEU LEU ASN VAL GLY HIS ILE GLU LYS MET GLN GLU GLY SEQRES 17 A 273 ILE VAL HIS VAL LEU ARG LEU HIS LEU GLN SER ASN HIS SEQRES 18 A 273 PRO ASP ASP ILE PHE LEU PHE PRO LYS LEU LEU GLN LYS SEQRES 19 A 273 MET ALA ASP LEU ARG GLN LEU VAL THR GLU HIS ALA GLN SEQRES 20 A 273 LEU VAL GLN ILE ILE LYS LYS THR GLU SER ASP ALA ALA SEQRES 21 A 273 LEU HIS PRO LEU LEU GLN GLU ILE TYR ARG ASP MET TYR HET EWR A 501 59 HETNAM EWR (2S)-2-ETHOXY-3-[4-[2-[2-METHYL-5-(4- HETNAM 2 EWR METHYLSULFANYLPHENYL)PYRROL-1- HETNAM 3 EWR YL]ETHOXY]PHENYL]PROPANOIC ACID FORMUL 2 EWR C25 H29 N O4 S FORMUL 3 HOH *11(H2 O) HELIX 1 AA1 THR A 200 PHE A 218 1 19 HELIX 2 AA2 ASN A 221 GLY A 231 1 11 HELIX 3 AA3 ASP A 243 THR A 253 1 11 HELIX 4 AA4 GLU A 267 LYS A 292 1 26 HELIX 5 AA5 ASP A 301 SER A 322 1 22 HELIX 6 AA6 ARG A 341 LEU A 347 1 7 HELIX 7 AA7 PRO A 350 ILE A 354 5 5 HELIX 8 AA8 MET A 355 ALA A 367 1 13 HELIX 9 AA9 ASP A 371 CYS A 384 1 14 HELIX 10 AB1 ASN A 393 HIS A 416 1 24 HELIX 11 AB2 PHE A 421 THR A 450 1 30 HELIX 12 AB3 HIS A 457 ARG A 465 1 9 SHEET 1 AA1 4 PHE A 239 ILE A 241 0 SHEET 2 AA1 4 GLY A 337 THR A 340 1 O PHE A 338 N ILE A 241 SHEET 3 AA1 4 GLY A 329 VAL A 332 -1 N VAL A 332 O GLY A 337 SHEET 4 AA1 4 MET A 325 ASN A 326 -1 N ASN A 326 O GLY A 329 CISPEP 1 LYS A 349 PRO A 350 0 -0.20 SITE 1 AC1 16 ILE A 272 PHE A 273 CYS A 275 CYS A 276 SITE 2 AC1 16 CYS A 278 THR A 279 SER A 280 TYR A 314 SITE 3 AC1 16 LEU A 321 MET A 330 VAL A 332 ALA A 333 SITE 4 AC1 16 TYR A 334 MET A 355 HIS A 440 TYR A 464 CRYST1 44.778 62.317 53.544 90.00 106.45 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 0.022332 0.000000 0.006592 0.00000 SCALE2 0.000000 0.016047 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019473 0.00000 CONECT 2045 2048 2070 2076 2077 CONECT 2046 2049 2051 2070 CONECT 2047 2050 2052 2070 CONECT 2048 2045 2071 2078 2079 CONECT 2049 2046 2050 2080 CONECT 2050 2047 2049 2081 CONECT 2051 2046 2057 2058 CONECT 2052 2047 2082 2083 2084 CONECT 2053 2054 2055 2085 2086 CONECT 2054 2053 2059 2060 CONECT 2055 2053 2066 2072 2087 CONECT 2056 2061 2062 2071 CONECT 2057 2051 2063 2088 CONECT 2058 2051 2064 2089 CONECT 2059 2054 2061 2090 CONECT 2060 2054 2062 2091 CONECT 2061 2056 2059 2092 CONECT 2062 2056 2060 2093 CONECT 2063 2057 2065 2094 CONECT 2064 2058 2065 2095 CONECT 2065 2063 2064 2075 CONECT 2066 2055 2073 2074 CONECT 2067 2068 2072 2096 2097 CONECT 2068 2067 2098 2099 2100 CONECT 2069 2075 2101 2102 2103 CONECT 2070 2045 2046 2047 CONECT 2071 2048 2056 CONECT 2072 2055 2067 CONECT 2073 2066 CONECT 2074 2066 CONECT 2075 2065 2069 CONECT 2076 2045 CONECT 2077 2045 CONECT 2078 2048 CONECT 2079 2048 CONECT 2080 2049 CONECT 2081 2050 CONECT 2082 2052 CONECT 2083 2052 CONECT 2084 2052 CONECT 2085 2053 CONECT 2086 2053 CONECT 2087 2055 CONECT 2088 2057 CONECT 2089 2058 CONECT 2090 2059 CONECT 2091 2060 CONECT 2092 2061 CONECT 2093 2062 CONECT 2094 2063 CONECT 2095 2064 CONECT 2096 2067 CONECT 2097 2067 CONECT 2098 2068 CONECT 2099 2068 CONECT 2100 2068 CONECT 2101 2069 CONECT 2102 2069 CONECT 2103 2069 MASTER 239 0 1 12 4 0 4 6 2079 1 59 21 END