HEADER NUCLEAR RECEPTOR 24-AUG-98 3PRG TITLE LIGAND BINDING DOMAIN OF HUMAN PEROXISOME PROLIFERATOR ACTIVATED TITLE 2 RECEPTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIGAND BINDING DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELLULAR_LOCATION: NUCLEUS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS THIAZOLIDINEDIONE, NUCLEAR RECEPTOR, TRANSCRIPTION FACTOR, ADIPOCYTE KEYWDS 2 DIFFERENTIATION EXPDTA X-RAY DIFFRACTION AUTHOR J.UPPENBERG,C.SVENSSON,M.JAKI,G.BERTILSSON,L.JENDEBERG,A.BERKENSTAM REVDAT 3 21-FEB-24 3PRG 1 REMARK REVDAT 2 24-FEB-09 3PRG 1 VERSN REVDAT 1 30-AUG-99 3PRG 0 JRNL AUTH J.UPPENBERG,C.SVENSSON,M.JAKI,G.BERTILSSON,L.JENDEBERG, JRNL AUTH 2 A.BERKENSTAM JRNL TITL CRYSTAL STRUCTURE OF THE LIGAND BINDING DOMAIN OF THE HUMAN JRNL TITL 2 NUCLEAR RECEPTOR PPARGAMMA. JRNL REF J.BIOL.CHEM. V. 273 31108 1998 JRNL REFN ISSN 0021-9258 JRNL PMID 9813012 JRNL DOI 10.1074/JBC.273.47.31108 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.3 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 8034 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) : 0.209 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT : 433 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.013 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1196 REMARK 3 BIN R VALUE (WORKING SET) : 0.3030 REMARK 3 BIN FREE R VALUE : 0.3750 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 80 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2139 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 64.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.03000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.33 REMARK 3 ESD FROM SIGMAA (A) : 0.39 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) : 0.55 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.64 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.780 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) : 3.240 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.570 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 6.880 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 9.920 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3PRG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000179113. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUN-98 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 9.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8069 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07000 REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.38800 REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS REMARK 200 SOFTWARE USED: SHARP, SOLOMON, CNS 0.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 9.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 78.44000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.62500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.62500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 117.66000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.62500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.62500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.22000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.62500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.62500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 117.66000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.62500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.62500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 39.22000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 78.44000 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 LYS A 263 REMARK 465 PHE A 264 REMARK 465 LYS A 265 REMARK 465 HIS A 266 REMARK 465 ILE A 267 REMARK 465 THR A 268 REMARK 465 PRO A 269 REMARK 465 LEU A 270 REMARK 465 GLN A 271 REMARK 465 GLU A 272 REMARK 465 GLN A 273 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NZ LYS A 301 NZ LYS A 301 8665 1.52 REMARK 500 REMARK 500 REMARK: NULL 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 245 87.61 -164.31 REMARK 500 LYS A 275 46.13 -94.74 REMARK 500 ARG A 357 146.97 -29.75 REMARK 500 LYS A 358 -62.80 -27.06 REMARK 500 THR A 459 -55.37 -160.42 REMARK 500 ASP A 475 31.36 -96.16 REMARK 500 REMARK 500 REMARK: NULL DBREF 3PRG A 204 477 UNP P37231 PPAT_HUMAN 202 475 SEQRES 1 A 278 ALA VAL HIS TYR LEU ASN PRO GLU SER ALA ASP LEU ARG SEQRES 2 A 278 ALA LEU ALA LYS HIS LEU TYR ASP SER TYR ILE LYS SER SEQRES 3 A 278 PHE PRO LEU THR LYS ALA LYS ALA ARG ALA ILE LEU THR SEQRES 4 A 278 GLY LYS THR THR ASP LYS SER PRO PHE VAL ILE TYR ASP SEQRES 5 A 278 MET ASN SER LEU MET MET GLY GLU ASP LYS ILE LYS PHE SEQRES 6 A 278 LYS HIS ILE THR PRO LEU GLN GLU GLN SER LYS GLU VAL SEQRES 7 A 278 ALA ILE ARG ILE PHE GLN GLY CYS GLN PHE ARG SER VAL SEQRES 8 A 278 GLU ALA VAL GLN GLU ILE THR GLU TYR ALA LYS SER ILE SEQRES 9 A 278 PRO GLY PHE VAL ASN LEU ASP LEU ASN ASP GLN VAL THR SEQRES 10 A 278 LEU LEU LYS TYR GLY VAL HIS GLU ILE ILE TYR THR MET SEQRES 11 A 278 LEU ALA SER LEU MET ASN LYS ASP GLY VAL LEU ILE SER SEQRES 12 A 278 GLU GLY GLN GLY PHE MET THR ARG GLU PHE LEU LYS SER SEQRES 13 A 278 LEU ARG LYS PRO PHE GLY ASP PHE MET GLU PRO LYS PHE SEQRES 14 A 278 GLU PHE ALA VAL LYS PHE ASN ALA LEU GLU LEU ASP ASP SEQRES 15 A 278 SER ASP LEU ALA ILE PHE ILE ALA VAL ILE ILE LEU SER SEQRES 16 A 278 GLY ASP ARG PRO GLY LEU LEU ASN VAL LYS PRO ILE GLU SEQRES 17 A 278 ASP ILE GLN ASP ASN LEU LEU GLN ALA LEU GLU LEU GLN SEQRES 18 A 278 LEU LYS LEU ASN HIS PRO GLU SER SER GLN LEU PHE ALA SEQRES 19 A 278 LYS LEU LEU GLN LYS MET THR ASP LEU ARG GLN ILE VAL SEQRES 20 A 278 THR GLU HIS VAL GLN LEU LEU GLN VAL ILE LYS LYS THR SEQRES 21 A 278 GLU THR ASP MET SER LEU HIS PRO LEU LEU GLN GLU ILE SEQRES 22 A 278 TYR LYS ASP LEU TYR HELIX 1 1 PRO A 206 SER A 225 1 20 HELIX 2 2 LYS A 230 LEU A 237 1 8 HELIX 3 3 MET A 252 GLY A 258 1 7 HELIX 4 4 VAL A 277 LYS A 301 1 25 HELIX 5 5 LEU A 311 LEU A 330 1 20 HELIX 6 6 ARG A 350 SER A 355 1 6 HELIX 7 7 GLU A 365 ASN A 375 1 11 HELIX 8 8 ASP A 381 ILE A 392 1 12 HELIX 9 9 LYS A 404 ASN A 424 1 21 HELIX 10 10 LEU A 431 LYS A 457 1 27 HELIX 11 11 PRO A 467 LYS A 474 1 8 SHEET 1 A 4 PHE A 247 ILE A 249 0 SHEET 2 A 4 GLY A 346 THR A 349 1 O PHE A 347 N ILE A 249 SHEET 3 A 4 GLY A 338 ILE A 341 -1 N VAL A 339 O MET A 348 SHEET 4 A 4 MET A 334 ASN A 335 -1 N ASN A 335 O GLY A 338 CRYST1 67.250 67.250 156.880 90.00 90.00 90.00 P 43 21 2 8 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 0.014870 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014870 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006374 0.00000