HEADER TRANSCRIPTION/TRANSCRIPTION ACTIVATOR 27-AUG-11 3TKM TITLE CRYSTAL STRUCTURE PPAR DELTA BINDING GW0742 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR DELTA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LBD, UNP RESIDUES 171-441; COMPND 5 SYNONYM: PPAR-DELTA, NUCI, NUCLEAR HORMONE RECEPTOR 1, NUC1, NUCLEAR COMPND 6 RECEPTOR SUBFAMILY 1 GROUP C MEMBER 2, PEROXISOME PROLIFERATOR- COMPND 7 ACTIVATED RECEPTOR BETA, PPAR-BETA; COMPND 8 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: PPARD, NR1C2, PPARB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS NUCLEAR RECEPTOR, TRANSCRIPTION, TRANSCRIPTION-TRANSCRIPTION KEYWDS 2 ACTIVATOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.B.B.TRIVELLA,F.H.BATISTA,I.POLIKARPOV REVDAT 3 13-SEP-23 3TKM 1 REMARK REVDAT 2 21-OCT-20 3TKM 1 REMARK SEQADV REVDAT 1 04-JUL-12 3TKM 0 JRNL AUTH F.A.BATISTA,D.B.TRIVELLA,A.BERNARDES,J.GRATIERI, JRNL AUTH 2 P.S.OLIVEIRA,A.C.FIGUEIRA,P.WEBB,I.POLIKARPOV JRNL TITL STRUCTURAL INSIGHTS INTO HUMAN PEROXISOME PROLIFERATOR JRNL TITL 2 ACTIVATED RECEPTOR DELTA (PPAR-DELTA) SELECTIVE LIGAND JRNL TITL 3 BINDING. JRNL REF PLOS ONE V. 7 33643 2012 JRNL REFN ESSN 1932-6203 JRNL PMID 22606221 JRNL DOI 10.1371/JOURNAL.PONE.0033643 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 2009_06_19_0104) 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 19139 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 977 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 24.3536 - 3.7314 0.99 2753 142 0.1733 0.1918 REMARK 3 2 3.7314 - 2.9634 0.99 2599 149 0.1857 0.2527 REMARK 3 3 2.9634 - 2.5893 1.00 2591 151 0.2039 0.2536 REMARK 3 4 2.5893 - 2.3528 1.00 2566 144 0.2043 0.2909 REMARK 3 5 2.3528 - 2.1842 0.99 2578 131 0.2189 0.2654 REMARK 3 6 2.1842 - 2.0555 0.99 2556 125 0.2326 0.2993 REMARK 3 7 2.0555 - 1.9530 0.98 2519 135 0.2530 0.3029 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 : 0.36 REMARK 3 B_SOL : 54.55 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.32030 REMARK 3 B22 (A**2) : 0.43350 REMARK 3 B33 (A**2) : -0.75380 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 2376 REMARK 3 ANGLE : 0.772 3235 REMARK 3 CHIRALITY : 0.046 362 REMARK 3 PLANARITY : 0.003 409 REMARK 3 DIHEDRAL : 15.035 904 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: NULL REMARK 4 REMARK 4 3TKM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000067594. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS REMARK 200 BEAMLINE : W01B-MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.4589 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19254 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09800 REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.43800 REMARK 200 FOR SHELL : 2.630 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: 3ET2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% (W/V) POLYETHYLENE GLYCOL (PEG) REMARK 280 8000, 200 MM KCL, 40 MM BIS-TRIS-PROPANE (PH 9.5), 6% PROPANOL, REMARK 280 AND 1 MM CACL2 AND DETERGENT N-OCTYL-B-D-THIOGLUCOSIDE (0.5 REMARK 280 MICROLITERS IN 5 MICROLITERS DROPS), VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 291K 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 17.73300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.14350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.38300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.14350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.73300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.38300 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 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 LYS A 229 REMARK 465 GLN A 230 REMARK 465 LEU A 231 REMARK 465 VAL A 232 REMARK 465 ASN A 233 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 LYS A 239 -50.78 -120.33 REMARK 500 SER A 269 2.36 85.22 REMARK 500 ASN A 366 74.02 -118.43 REMARK 500 GLU A 424 65.15 -103.40 REMARK 500 MET A 440 -9.49 -148.36 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 GW0 A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 442 DBREF 3TKM A 171 441 UNP Q03181 PPARD_HUMAN 171 441 SEQADV 3TKM GLY A 167 UNP Q03181 EXPRESSION TAG SEQADV 3TKM SER A 168 UNP Q03181 EXPRESSION TAG SEQADV 3TKM HIS A 169 UNP Q03181 EXPRESSION TAG SEQADV 3TKM MET A 170 UNP Q03181 EXPRESSION TAG SEQRES 1 A 275 GLY SER HIS MET GLN VAL ALA ASP LEU LYS ALA PHE SER SEQRES 2 A 275 LYS HIS ILE TYR ASN ALA TYR LEU LYS ASN PHE ASN MET SEQRES 3 A 275 THR LYS LYS LYS ALA ARG SER ILE LEU THR GLY LYS ALA SEQRES 4 A 275 SER HIS THR ALA PRO PHE VAL ILE HIS ASP ILE GLU THR SEQRES 5 A 275 LEU TRP GLN ALA GLU LYS GLY LEU VAL TRP LYS GLN LEU SEQRES 6 A 275 VAL ASN GLY LEU PRO PRO TYR LYS GLU ILE SER VAL HIS SEQRES 7 A 275 VAL PHE TYR ARG CYS GLN CYS THR THR VAL GLU THR VAL SEQRES 8 A 275 ARG GLU LEU THR GLU PHE ALA LYS SER ILE PRO SER PHE SEQRES 9 A 275 SER SER LEU PHE LEU ASN ASP GLN VAL THR LEU LEU LYS SEQRES 10 A 275 TYR GLY VAL HIS GLU ALA ILE PHE ALA MET LEU ALA SER SEQRES 11 A 275 ILE VAL ASN LYS ASP GLY LEU LEU VAL ALA ASN GLY SER SEQRES 12 A 275 GLY PHE VAL THR ARG GLU PHE LEU ARG SER LEU ARG LYS SEQRES 13 A 275 PRO PHE SER ASP ILE ILE GLU PRO LYS PHE GLU PHE ALA SEQRES 14 A 275 VAL LYS PHE ASN ALA LEU GLU LEU ASP ASP SER ASP LEU SEQRES 15 A 275 ALA LEU PHE ILE ALA ALA ILE ILE LEU CYS GLY ASP ARG SEQRES 16 A 275 PRO GLY LEU MET ASN VAL PRO ARG VAL GLU ALA ILE GLN SEQRES 17 A 275 ASP THR ILE LEU ARG ALA LEU GLU PHE HIS LEU GLN ALA SEQRES 18 A 275 ASN HIS PRO ASP ALA GLN TYR LEU PHE PRO LYS LEU LEU SEQRES 19 A 275 GLN LYS MET ALA ASP LEU ARG GLN LEU VAL THR GLU HIS SEQRES 20 A 275 ALA GLN MET MET GLN ARG ILE LYS LYS THR GLU THR GLU SEQRES 21 A 275 THR SER LEU HIS PRO LEU LEU GLN GLU ILE TYR LYS ASP SEQRES 22 A 275 MET TYR HET GW0 A 1 31 HET GOL A 442 6 HETNAM GW0 {4-[({2-[3-FLUORO-4-(TRIFLUOROMETHYL)PHENYL]-4-METHYL- HETNAM 2 GW0 1,3-THIAZOL-5-YL}METHYL)SULFANYL]-2- HETNAM 3 GW0 METHYLPHENOXY}ACETIC ACID HETNAM GOL GLYCEROL HETSYN GW0 GW 0742 HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GW0 C21 H17 F4 N O3 S2 FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *158(H2 O) HELIX 1 1 GLN A 171 PHE A 190 1 20 HELIX 2 2 THR A 193 THR A 202 1 10 HELIX 3 3 ASP A 215 LEU A 226 1 12 HELIX 4 4 GLU A 240 SER A 266 1 27 HELIX 5 5 PHE A 274 ALA A 295 1 22 HELIX 6 6 ALA A 306 GLY A 308 5 3 HELIX 7 7 ARG A 314 SER A 319 1 6 HELIX 8 8 PHE A 324 ALA A 340 1 17 HELIX 9 9 ASP A 344 LEU A 357 1 14 HELIX 10 10 ASN A 366 HIS A 389 1 24 HELIX 11 11 TYR A 394 GLU A 424 1 31 HELIX 12 12 HIS A 430 ASP A 439 1 10 SHEET 1 A 4 PHE A 211 ILE A 213 0 SHEET 2 A 4 GLY A 310 THR A 313 1 O PHE A 311 N ILE A 213 SHEET 3 A 4 GLY A 302 VAL A 305 -1 N VAL A 305 O GLY A 310 SHEET 4 A 4 VAL A 298 ASN A 299 -1 N ASN A 299 O GLY A 302 CISPEP 1 LYS A 322 PRO A 323 0 5.09 SITE 1 AC1 12 PHE A 246 ARG A 248 CYS A 249 THR A 253 SITE 2 AC1 12 HIS A 287 LEU A 294 VAL A 305 VAL A 312 SITE 3 AC1 12 ILE A 327 HIS A 413 LEU A 433 TYR A 437 SITE 1 AC2 4 HOH A 65 MET A 365 ARG A 369 THR A 376 CRYST1 35.466 74.766 96.287 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 0.028196 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013375 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010386 0.00000