HEADER TRANSCRIPTION 23-MAR-20 7BQ3
TITLE X-RAY STRUCTURE OF HUMAN PPARALPHA LIGAND BINDING DOMAIN-GW7647-SRC1
TITLE 2 COACTIVATOR PEPTIDE CO-CRYSTALS OBTAINED BY DELIPIDATION AND CO-
TITLE 3 CRYSTALLIZATION
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR ALPHA;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: 15-MERIC PEPTIDE FROM NUCLEAR RECEPTOR COACTIVATOR 1;
COMPND 7 CHAIN: B;
COMPND 8 EC: 2.3.1.48;
COMPND 9 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;
SOURCE 8 MOL_ID: 2;
SOURCE 9 SYNTHETIC: YES;
SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 11 ORGANISM_COMMON: HUMAN;
SOURCE 12 ORGANISM_TAXID: 9606
KEYWDS NUCLEAR RECEPTOR, PROTEIN-LIGAND COMPLEX, PPAR, TRANSCRIPTION
EXPDTA X-RAY DIFFRACTION
AUTHOR S.KAMATA,R.ISHIKAWA,M.AKAHANE,T.OYAMA,I.ISHII
REVDAT 3 29-NOV-23 7BQ3 1 REMARK
REVDAT 2 02-DEC-20 7BQ3 1 JRNL
REVDAT 1 11-NOV-20 7BQ3 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. 1.98 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) : 1.98
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.20
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.940
REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3
REMARK 3 NUMBER OF REFLECTIONS : 20722
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.195
REMARK 3 R VALUE (WORKING SET) : 0.193
REMARK 3 FREE R VALUE : 0.237
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.810
REMARK 3 FREE R VALUE TEST SET COUNT : 950
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 40.1990 - 4.6536 0.98 2926 167 0.1518 0.1710
REMARK 3 2 4.6536 - 3.6945 0.94 2823 130 0.1453 0.2049
REMARK 3 3 3.6945 - 3.2277 0.97 2901 142 0.1902 0.2153
REMARK 3 4 3.2277 - 2.9327 0.98 2940 134 0.2199 0.2868
REMARK 3 5 2.9327 - 2.7226 0.97 2870 143 0.2251 0.2564
REMARK 3 6 2.7226 - 2.5621 0.98 2938 159 0.2243 0.3113
REMARK 3 7 2.5621 - 2.4338 0.97 2911 147 0.2148 0.2514
REMARK 3 8 2.4338 - 2.3279 0.97 2881 162 0.2019 0.2123
REMARK 3 9 2.3279 - 2.2382 0.95 2851 146 0.2296 0.3130
REMARK 3 10 2.2382 - 2.1610 0.93 2826 114 0.2259 0.3486
REMARK 3 11 2.1610 - 2.0934 0.95 2832 140 0.2434 0.2752
REMARK 3 12 2.0934 - 2.0336 0.96 2843 155 0.2516 0.2904
REMARK 3 13 2.0336 - 1.9801 0.96 2865 150 0.2834 0.3644
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) : 0.260
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.060
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 31.17
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.18
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 : 0.014 2251
REMARK 3 ANGLE : 1.381 3033
REMARK 3 CHIRALITY : 0.071 342
REMARK 3 PLANARITY : 0.008 383
REMARK 3 DIHEDRAL : 15.917 1377
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 7BQ3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-MAR-20.
REMARK 100 THE DEPOSITION ID IS D_1300016264.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 07-MAR-20
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 : 20737
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980
REMARK 200 RESOLUTION RANGE LOW (A) : 46.240
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2
REMARK 200 DATA REDUNDANCY : 3.400
REMARK 200 R MERGE (I) : 0.03500
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9
REMARK 200 DATA REDUNDANCY IN SHELL : 3.40
REMARK 200 R MERGE FOR SHELL (I) : 0.37700
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000
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: 3SP6
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 46.84
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS (PH 8.5), 25%(W/V) PEG3350,
REMARK 280 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 30.74700
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1270 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 12830 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 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 465 ASN A 235
REMARK 465 ASN A 236
REMARK 465 LEU A 258
REMARK 465 VAL A 259
REMARK 465 ALA A 260
REMARK 465 ASN A 261
REMARK 465 GLY A 262
REMARK 465 ILE A 263
REMARK 465 GLN A 264
REMARK 465 LEU B 683
REMARK 465 THR B 684
REMARK 465 GLU B 685
REMARK 465 GLY B 697
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 ALA A 256 -81.53 -66.62
REMARK 500 LYS A 266 -166.26 -101.92
REMARK 500 ASN A 393 73.55 -105.93
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 2VN A 501
DBREF 7BQ3 A 200 468 UNP Q07869 PPARA_HUMAN 200 468
DBREF 7BQ3 B 683 697 UNP Q15788 NCOA1_HUMAN 683 697
SEQADV 7BQ3 GLY A 196 UNP Q07869 EXPRESSION TAG
SEQADV 7BQ3 SER A 197 UNP Q07869 EXPRESSION TAG
SEQADV 7BQ3 HIS A 198 UNP Q07869 EXPRESSION TAG
SEQADV 7BQ3 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
SEQRES 1 B 15 LEU THR GLU ARG HIS LYS ILE LEU HIS ARG LEU LEU GLN
SEQRES 2 B 15 GLU GLY
HET 2VN A 501 80
HETNAM 2VN 2-[(4-{2-[(4-CYCLOHEXYLBUTYL)(CYCLOHEXYLCARBAMOYL)
HETNAM 2 2VN AMINO]ETHYL}PHENYL)SULFANYL]-2-METHYLPROPANOIC ACID
FORMUL 3 2VN C29 H46 N2 O3 S
FORMUL 4 HOH *41(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 GLU A 267 ALA A 293 1 27
HELIX 5 AA5 GLY A 296 LEU A 300 5 5
HELIX 6 AA6 ASP A 301 SER A 322 1 22
HELIX 7 AA7 ARG A 341 LEU A 347 1 7
HELIX 8 AA8 PRO A 350 ILE A 354 5 5
HELIX 9 AA9 MET A 355 ALA A 367 1 13
HELIX 10 AB1 ASP A 371 CYS A 384 1 14
HELIX 11 AB2 ASN A 393 HIS A 416 1 24
HELIX 12 AB3 PHE A 421 GLU A 451 1 31
HELIX 13 AB4 HIS A 457 ARG A 465 1 9
HELIX 14 AB5 HIS B 687 GLU B 696 1 10
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 1.41
SITE 1 AC1 11 PHE A 273 CYS A 276 GLN A 277 THR A 279
SITE 2 AC1 11 SER A 280 TYR A 314 MET A 355 HIS A 440
SITE 3 AC1 11 TYR A 464 HOH A 613 HOH A 617
CRYST1 46.329 61.494 53.218 90.00 93.48 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 0.021585 0.000000 0.001312 0.00000
SCALE2 0.000000 0.016262 0.000000 0.00000
SCALE3 0.000000 0.000000 0.018825 0.00000