HEADER TRANSCRIPTION 28-DEC-21 7WGP TITLE X-RAY STRUCTURE OF HUMAN PPAR GAMMA LIGAND BINDING DOMAIN-FENOFIBRIC TITLE 2 ACID CO-CRYSTALS OBTAINED BY CO-CRYSTALLIZATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOFORM 1 OF PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR COMPND 3 GAMMA; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: PPAR-GAMMA; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 15-MERIC PEPTIDE FROM NUCLEAR RECEPTOR COACTIVATOR 1; COMPND 9 CHAIN: B; COMPND 10 EC: 2.3.1.48; COMPND 11 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: PPARG; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS NUCLEAR RECEPTOR, PROTEIN-LIGAND COMPLEX, PPAR, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR S.KAMATA,A.HONDA,M.AKAHANE,Y.MACHIDA,K.UCHII,Y.SHIIYAMA,R.MASUDA, AUTHOR 2 T.OYAMA,I.ISHII REVDAT 2 29-NOV-23 7WGP 1 REMARK REVDAT 1 25-MAY-22 7WGP 0 JRNL AUTH A.HONDA,S.KAMATA,M.AKAHANE,Y.MACHIDA,K.UCHII,Y.SHIIYAMA, JRNL AUTH 2 Y.HABU,S.MIYAWAKI,C.KANEKO,T.OYAMA,I.ISHII JRNL TITL FUNCTIONAL AND STRUCTURAL INSIGHTS INTO HUMAN PPAR ALPHA / JRNL TITL 2 DELTA / GAMMA SUBTYPE SELECTIVITY OF BEZAFIBRATE, FENOFIBRIC JRNL TITL 3 ACID, AND PEMAFIBRATE. JRNL REF INT J MOL SCI V. 23 2022 JRNL REFN ESSN 1422-0067 JRNL PMID 35563117 JRNL DOI 10.3390/IJMS23094726 REMARK 2 REMARK 2 RESOLUTION. 2.53 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 13870 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.660 REMARK 3 FREE R VALUE TEST SET COUNT : 1192 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 44.7180 - 5.2608 0.99 2715 154 0.1950 0.2444 REMARK 3 2 5.2608 - 4.1766 1.00 2750 123 0.1692 0.1993 REMARK 3 3 4.1766 - 3.6489 1.00 2726 153 0.1879 0.2262 REMARK 3 4 3.6489 - 3.3154 0.99 2712 144 0.2246 0.3189 REMARK 3 5 3.3154 - 3.0779 0.99 2736 121 0.2548 0.3719 REMARK 3 6 3.0779 - 2.8964 0.99 2736 115 0.2644 0.4024 REMARK 3 7 2.8964 - 2.7514 0.99 2735 117 0.2556 0.3034 REMARK 3 8 2.7514 - 2.6316 0.99 2695 151 0.2608 0.3441 REMARK 3 9 2.6316 - 2.5303 0.94 2601 114 0.2672 0.3194 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 65.16 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 : 0.005 2363 REMARK 3 ANGLE : 0.794 3187 REMARK 3 CHIRALITY : 0.042 358 REMARK 3 PLANARITY : 0.004 402 REMARK 3 DIHEDRAL : 16.317 1431 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 7WGP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1300025760. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUN-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 : 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 : 13952 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.530 REMARK 200 RESOLUTION RANGE LOW (A) : 46.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.37400 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 2.7.16 REMARK 200 STARTING MODEL: 1WM0 REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS REMARK 200 COLUMNS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS (PH 8.0), 1.1 M TRISODIUM REMARK 280 CITRATE, VAPOR DIFFUSION, TEMPERATURE 293K 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 25.08050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.08550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.23200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.08550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.08050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.23200 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 199 REMARK 465 SER A 200 REMARK 465 HIS A 201 REMARK 465 THR A 242 REMARK 465 ASP A 243 REMARK 465 LYS A 244 REMARK 465 GLU A 460 REMARK 465 THR A 461 REMARK 465 ASP A 462 REMARK 465 MET A 463 REMARK 465 LEU B 600 REMARK 465 THR B 601 REMARK 465 GLU B 602 REMARK 465 GLY B 614 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 MET A 202 CG SD CE REMARK 470 GLU A 343 CG CD OE1 OE2 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 PRO A 206 -132.60 -84.57 REMARK 500 LYS A 240 99.61 -49.78 REMARK 500 GLU A 276 89.24 -179.27 REMARK 500 ASN A 335 -163.53 -125.07 REMARK 500 LYS A 358 -145.59 52.73 REMARK 500 LEU A 393 51.46 -103.85 REMARK 500 SER A 428 96.72 -169.86 REMARK 500 LYS A 458 34.36 -83.35 REMARK 500 REMARK 500 REMARK: NULL DBREF1 7WGP A 203 477 UNP PPARG-2_HUMAN DBREF2 7WGP A P37231-2 203 477 DBREF 7WGP B 600 614 UNP Q15788 NCOA1_HUMAN 683 697 SEQADV 7WGP GLY A 199 UNP P37231-2 EXPRESSION TAG SEQADV 7WGP SER A 200 UNP P37231-2 EXPRESSION TAG SEQADV 7WGP HIS A 201 UNP P37231-2 EXPRESSION TAG SEQADV 7WGP MET A 202 UNP P37231-2 EXPRESSION TAG SEQRES 1 A 279 GLY SER HIS MET GLN LEU ASN PRO GLU SER ALA ASP LEU SEQRES 2 A 279 ARG ALA LEU ALA LYS HIS LEU TYR ASP SER TYR ILE LYS SEQRES 3 A 279 SER PHE PRO LEU THR LYS ALA LYS ALA ARG ALA ILE LEU SEQRES 4 A 279 THR GLY LYS THR THR ASP LYS SER PRO PHE VAL ILE TYR SEQRES 5 A 279 ASP MET ASN SER LEU MET MET GLY GLU ASP LYS ILE LYS SEQRES 6 A 279 PHE LYS HIS ILE THR PRO LEU GLN GLU GLN SER LYS GLU SEQRES 7 A 279 VAL ALA ILE ARG ILE PHE GLN GLY CYS GLN PHE ARG SER SEQRES 8 A 279 VAL GLU ALA VAL GLN GLU ILE THR GLU TYR ALA LYS SER SEQRES 9 A 279 ILE PRO GLY PHE VAL ASN LEU ASP LEU ASN ASP GLN VAL SEQRES 10 A 279 THR LEU LEU LYS TYR GLY VAL HIS GLU ILE ILE TYR THR SEQRES 11 A 279 MET LEU ALA SER LEU MET ASN LYS ASP GLY VAL LEU ILE SEQRES 12 A 279 SER GLU GLY GLN GLY PHE MET THR ARG GLU PHE LEU LYS SEQRES 13 A 279 SER LEU ARG LYS PRO PHE GLY ASP PHE MET GLU PRO LYS SEQRES 14 A 279 PHE GLU PHE ALA VAL LYS PHE ASN ALA LEU GLU LEU ASP SEQRES 15 A 279 ASP SER ASP LEU ALA ILE PHE ILE ALA VAL ILE ILE LEU SEQRES 16 A 279 SER GLY ASP ARG PRO GLY LEU LEU ASN VAL LYS PRO ILE SEQRES 17 A 279 GLU ASP ILE GLN ASP ASN LEU LEU GLN ALA LEU GLU LEU SEQRES 18 A 279 GLN LEU LYS LEU ASN HIS PRO GLU SER SER GLN LEU PHE SEQRES 19 A 279 ALA LYS LEU LEU GLN LYS MET THR ASP LEU ARG GLN ILE SEQRES 20 A 279 VAL THR GLU HIS VAL GLN LEU LEU GLN VAL ILE LYS LYS SEQRES 21 A 279 THR GLU THR ASP MET SER LEU HIS PRO LEU LEU GLN GLU SEQRES 22 A 279 ILE TYR LYS ASP LEU TYR SEQRES 1 B 15 LEU THR GLU ARG HIS LYS ILE LEU HIS ARG LEU LEU GLN SEQRES 2 B 15 GLU GLY HET F5A A 501 36 HET F5A A 502 36 HET F5A A 503 36 HETNAM F5A 2-[4-(4-CHLOROBENZENE-1-CARBONYL)PHENOXY]-2- HETNAM 2 F5A METHYLPROPANOIC ACID FORMUL 3 F5A 3(C17 H15 CL O4) HELIX 1 AA1 SER A 208 PHE A 226 1 19 HELIX 2 AA2 THR A 229 GLY A 239 1 11 HELIX 3 AA3 ASP A 251 ILE A 262 1 12 HELIX 4 AA4 GLU A 276 SER A 302 1 27 HELIX 5 AA5 GLY A 305 LEU A 309 5 5 HELIX 6 AA6 ASP A 310 SER A 332 1 23 HELIX 7 AA7 ARG A 350 LEU A 356 1 7 HELIX 8 AA8 ARG A 357 PHE A 363 5 7 HELIX 9 AA9 MET A 364 LEU A 377 1 14 HELIX 10 AB1 ASP A 380 LEU A 393 1 14 HELIX 11 AB2 VAL A 403 HIS A 425 1 23 HELIX 12 AB3 GLN A 430 LYS A 458 1 29 HELIX 13 AB4 HIS A 466 LYS A 474 1 9 HELIX 14 AB5 HIS B 604 GLN B 612 1 9 SHEET 1 AA1 3 PHE A 247 ILE A 249 0 SHEET 2 AA1 3 GLY A 346 THR A 349 1 O PHE A 347 N ILE A 249 SHEET 3 AA1 3 GLY A 338 ILE A 341 -1 N ILE A 341 O GLY A 346 CRYST1 50.161 64.464 124.171 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 0.019936 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015513 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008053 0.00000