HEADER TRANSCRIPTION 10-FEB-20 6LX8 TITLE X-RAY STRUCTURE OF HUMAN PPARALPHA LIGAND BINDING DOMAIN-OLEIC ACID TITLE 2 CO-CRYSTALS OBTAINED BY DELIPIDATION AND CROSS-SEEDING 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,K.SAITO,A.HONDA,R.ISHIKAWA,T.OYAMA,I.ISHII REVDAT 3 29-NOV-23 6LX8 1 REMARK REVDAT 2 02-DEC-20 6LX8 1 JRNL REVDAT 1 11-NOV-20 6LX8 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. 1.54 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) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.920 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 40815 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.690 REMARK 3 FREE R VALUE TEST SET COUNT : 3650 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 43.0600 - 4.5605 0.99 2912 150 0.1666 0.1685 REMARK 3 2 4.5605 - 3.6204 1.00 2961 144 0.1461 0.1473 REMARK 3 3 3.6204 - 3.1629 0.95 2776 150 0.1757 0.1880 REMARK 3 4 3.1629 - 2.8738 0.96 2860 138 0.2002 0.2193 REMARK 3 5 2.8738 - 2.6678 0.98 2829 160 0.1840 0.2102 REMARK 3 6 2.6678 - 2.5106 0.98 2913 144 0.1894 0.1805 REMARK 3 7 2.5106 - 2.3849 0.99 2911 134 0.1778 0.2014 REMARK 3 8 2.3849 - 2.2810 0.98 2911 145 0.1742 0.2097 REMARK 3 9 2.2810 - 2.1932 0.98 2908 127 0.1651 0.1732 REMARK 3 10 2.1932 - 2.1176 0.98 2912 123 0.1757 0.1980 REMARK 3 11 2.1176 - 2.0513 0.98 2914 130 0.1782 0.2116 REMARK 3 12 2.0513 - 1.9927 0.98 2942 160 0.1858 0.2105 REMARK 3 13 1.9927 - 1.9403 0.98 2862 132 0.1769 0.2360 REMARK 3 14 1.9403 - 1.8929 0.97 2862 133 0.1784 0.2045 REMARK 3 15 1.8929 - 1.8499 0.96 2816 154 0.1788 0.2130 REMARK 3 16 1.8499 - 1.8105 0.95 2802 141 0.1849 0.1842 REMARK 3 17 1.8105 - 1.7743 0.94 2741 150 0.1946 0.2105 REMARK 3 18 1.7743 - 1.7408 0.94 2811 141 0.2001 0.2555 REMARK 3 19 1.7408 - 1.7097 0.96 2822 150 0.2100 0.2496 REMARK 3 20 1.7097 - 1.6807 0.95 2840 137 0.2041 0.2277 REMARK 3 21 1.6807 - 1.6536 0.96 2799 125 0.2097 0.2455 REMARK 3 22 1.6536 - 1.6282 0.96 2850 135 0.2019 0.2618 REMARK 3 23 1.6282 - 1.6042 0.95 2784 122 0.2075 0.2488 REMARK 3 24 1.6042 - 1.5816 0.96 2878 149 0.2166 0.2177 REMARK 3 25 1.5816 - 1.5603 0.96 2797 141 0.2114 0.2445 REMARK 3 26 1.5603 - 1.5400 0.94 2784 135 0.2315 0.2632 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.74 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.87 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 2258 REMARK 3 ANGLE : 1.149 3052 REMARK 3 CHIRALITY : 0.067 343 REMARK 3 PLANARITY : 0.007 396 REMARK 3 DIHEDRAL : 13.142 1391 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 6LX8 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_1300015616. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-18 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-17A 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 EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40834 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 REMARK 200 RESOLUTION RANGE LOW (A) : 43.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.44300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 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 (%): 45.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES (PH 7.0), 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 30.76900 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: 260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 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 THR A 200 REMARK 465 ALA A 201 REMARK 465 LYS A 232 REMARK 465 ALA A 233 REMARK 465 SER A 234 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 ILE A 263 CG1 CG2 CD1 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 VAL A 255 57.99 -142.13 REMARK 500 CYS A 384 58.95 -92.42 REMARK 500 ASN A 393 67.71 -117.73 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 GOL A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OLA A 502 DBREF 6LX8 A 200 468 UNP Q07869 PPARA_HUMAN 200 468 SEQADV 6LX8 GLY A 196 UNP Q07869 EXPRESSION TAG SEQADV 6LX8 SER A 197 UNP Q07869 EXPRESSION TAG SEQADV 6LX8 HIS A 198 UNP Q07869 EXPRESSION TAG SEQADV 6LX8 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 GOL A 501 14 HET OLA A 502 53 HETNAM GOL GLYCEROL HETNAM OLA OLEIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 OLA C18 H34 O2 FORMUL 4 HOH *181(H2 O) HELIX 1 AA1 ASP A 202 PHE A 218 1 17 HELIX 2 AA2 ASN A 221 GLY A 231 1 11 HELIX 3 AA3 ASP A 243 VAL A 255 1 13 HELIX 4 AA4 ALA A 256 ALA A 260 5 5 HELIX 5 AA5 ASN A 261 ASN A 265 5 5 HELIX 6 AA6 GLU A 267 LYS A 292 1 26 HELIX 7 AA7 ASP A 301 SER A 322 1 22 HELIX 8 AA8 ARG A 341 LEU A 347 1 7 HELIX 9 AA9 PRO A 350 ILE A 354 5 5 HELIX 10 AB1 MET A 355 LEU A 368 1 14 HELIX 11 AB2 ASP A 371 CYS A 384 1 14 HELIX 12 AB3 ASN A 393 HIS A 416 1 24 HELIX 13 AB4 PHE A 421 GLU A 451 1 31 HELIX 14 AB5 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 MET A 330 O ILE A 339 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 4.25 SITE 1 AC1 7 LYS A 222 ARG A 226 LEU A 229 SER A 323 SITE 2 AC1 7 MET A 325 ASN A 326 ASN A 366 SITE 1 AC2 8 CYS A 276 SER A 280 TYR A 314 VAL A 332 SITE 2 AC2 8 HIS A 440 LEU A 460 TYR A 464 HOH A 756 CRYST1 44.904 61.538 52.969 90.00 106.47 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 0.022270 0.000000 0.006585 0.00000 SCALE2 0.000000 0.016250 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019687 0.00000