HEADER TRANSCRIPTION 25-SEP-11 3VI8 TITLE HUMAN PPAR ALPHA LIGAND BINDING DOMAIN IN COMPLEX WITH A SYNTHETIC TITLE 2 AGONIST APHM13 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR ALPHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIGAND BINDING DOMAIN; COMPND 5 SYNONYM: PPAR-ALPHA, NUCLEAR RECEPTOR SUBFAMILY 1 GROUP C MEMBER 1; COMPND 6 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: PPARA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS NUCLEAR RECEPTOR, PROTEIN-LIGAND COMPLEX, PPAR, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR T.OYAMA,H.MIYACHI,K.MORIKAWA REVDAT 3 08-NOV-23 3VI8 1 REMARK SEQADV REVDAT 2 02-MAR-16 3VI8 1 TITLE REVDAT 1 29-AUG-12 3VI8 0 JRNL AUTH N.KUWABARA,T.OYAMA,D.TOMIOKA,M.OHASHI,J.YANAGISAWA, JRNL AUTH 2 T.SHIMIZU,H.MIYACHI JRNL TITL PEROXISOME PROLIFERATOR-ACTIVATED RECEPTORS (PPARS) HAVE JRNL TITL 2 MULTIPLE BINDING POINTS THAT ACCOMMODATE LIGANDS IN VARIOUS JRNL TITL 3 CONFORMATIONS: PHENYLPROPANOIC ACID-TYPE PPAR LIGANDS BIND JRNL TITL 4 TO PPAR IN DIFFERENT CONFORMATIONS, DEPENDING ON THE SUBTYPE JRNL REF J.MED.CHEM. V. 55 893 2012 JRNL REFN ISSN 0022-2623 JRNL PMID 22185225 JRNL DOI 10.1021/JM2014293 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 254506.140 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 26414 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1287 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3707 REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE : 0.3080 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 169 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2054 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 172 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.46000 REMARK 3 B22 (A**2) : -3.13000 REMARK 3 B33 (A**2) : -3.32000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 6.06000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.19 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.21 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.180 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.130 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.700 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.880 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.730 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 52.60 REMARK 3 REMARK 3 NCS MODEL : NONE REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : 13S_PAR.TXT REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : 13S_TOP.TXT REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3VI8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000095076. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 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 : FIXED EXIT SI 111 DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27254 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: CNS REMARK 200 STARTING MODEL: PDB ENTRY 2ZNN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 0.1M HEPES, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, 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 30.65200 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 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 GLY A 231 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 PRO A 237 REMARK 465 ILE A 263 REMARK 465 GLN A 264 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 393 77.87 -113.44 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 13M A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZNN RELATED DB: PDB DBREF 3VI8 A 200 468 UNP Q07869 PPARA_HUMAN 200 468 SEQADV 3VI8 GLY A 196 UNP Q07869 EXPRESSION TAG SEQADV 3VI8 SER A 197 UNP Q07869 EXPRESSION TAG SEQADV 3VI8 HIS A 198 UNP Q07869 EXPRESSION TAG SEQADV 3VI8 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 13M A 1 35 HETNAM 13M (2S)-2-(4-METHOXY-3-{[(PYREN-1-YLCARBONYL) HETNAM 2 13M AMINO]METHYL}BENZYL)BUTANOIC ACID FORMUL 2 13M C30 H27 N O4 FORMUL 3 HOH *172(H2 O) HELIX 1 1 ASP A 202 PHE A 218 1 17 HELIX 2 2 ASN A 221 SER A 230 1 10 HELIX 3 3 ASP A 243 VAL A 255 1 13 HELIX 4 4 ALA A 256 ALA A 260 5 5 HELIX 5 5 GLU A 267 ALA A 291 1 25 HELIX 6 6 LYS A 292 ILE A 294 5 3 HELIX 7 7 ASP A 301 SER A 322 1 22 HELIX 8 8 ARG A 341 LEU A 347 1 7 HELIX 9 9 PHE A 351 ALA A 367 1 17 HELIX 10 10 ASP A 371 CYS A 384 1 14 HELIX 11 11 ASN A 393 HIS A 416 1 24 HELIX 12 12 PHE A 421 GLU A 451 1 31 HELIX 13 13 HIS A 457 ARG A 465 1 9 SHEET 1 A 4 PHE A 239 ILE A 241 0 SHEET 2 A 4 GLY A 337 THR A 340 1 O PHE A 338 N ILE A 241 SHEET 3 A 4 GLY A 329 VAL A 332 -1 N MET A 330 O ILE A 339 SHEET 4 A 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 0.07 SITE 1 AC1 14 PHE A 273 CYS A 276 THR A 279 SER A 280 SITE 2 AC1 14 TYR A 314 MET A 330 VAL A 332 ALA A 333 SITE 3 AC1 14 ILE A 339 MET A 355 HIS A 440 LEU A 460 SITE 4 AC1 14 TYR A 464 HOH A1060 CRYST1 44.368 61.304 53.179 90.00 106.95 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 0.022539 0.000000 0.006871 0.00000 SCALE2 0.000000 0.016312 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019659 0.00000