HEADER TRANSCRIPTION 13-NOV-19 6LB6 TITLE CRYSTAL STRUCTURE OF DIMERIC RXR-LBD COMPLEXED WITH PARTIAL AGONIST TITLE 2 NET-4IB AND TIF2 CO-ACTIVATOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOIC ACID RECEPTOR RXR-ALPHA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NUCLEAR RECEPTOR SUBFAMILY 2 GROUP B MEMBER 1,RETINOID X COMPND 5 RECEPTOR ALPHA; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: NUCLEAR RECEPTOR COACTIVATOR 2; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: NCOA-2,CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 75,BHLHE75, COMPND 11 TRANSCRIPTIONAL INTERMEDIARY FACTOR 2,HTIF2; COMPND 12 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: RXRA, NR2B1; 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: PET28A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS NUCLEAR RECEPTOR, RETINOID X RECEPTOR ALPHA, ACTIVE FORM, CO-FACTORS, KEYWDS 2 TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR D.IMAI,N.NUMOTO,S.NAKANO,H.KAKUTA,N.ITO REVDAT 3 22-NOV-23 6LB6 1 REMARK REVDAT 2 25-NOV-20 6LB6 1 REMARK REVDAT 1 18-NOV-20 6LB6 0 JRNL AUTH D.IMAI,N.NUMOTO,S.NAKANO,H.KAKUTA,N.ITO JRNL TITL CRYSTAL STRUCTURE OF DIMERIC RXR-LBD COMPLEXED WITH PARTIAL JRNL TITL 2 AGONIST NET-4IB AND TIF2 CO-ACTIVATOR JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 10034 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 499 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 27.8000 - 3.8100 1.00 2503 132 0.1968 0.2072 REMARK 3 2 3.8100 - 3.0200 1.00 2375 125 0.2358 0.2954 REMARK 3 3 3.0200 - 2.6400 1.00 2327 121 0.2667 0.3376 REMARK 3 4 2.6400 - 2.4000 1.00 2330 121 0.2801 0.3565 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) : 0.285 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.157 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 51.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.35 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 : 0.002 1826 REMARK 3 ANGLE : 0.487 2471 REMARK 3 CHIRALITY : 0.036 283 REMARK 3 PLANARITY : 0.003 315 REMARK 3 DIHEDRAL : 14.327 1130 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 6LB6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1300014490. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-OCT-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10048 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11800 REMARK 200 FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 12.73 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 1.46600 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 REMARK 200 STARTING MODEL: 6LB4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M IMIDAZOLE 20 % PEG6000, PH 7.0, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 55.59700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 32.84900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 32.84900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 83.39550 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 32.84900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 32.84900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 27.79850 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 32.84900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.84900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 83.39550 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 32.84900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.84900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 27.79850 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 55.59700 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 222.38800 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 220 REMARK 465 SER A 221 REMARK 465 SER A 222 REMARK 465 HIS A 223 REMARK 465 SER A 224 REMARK 465 SER A 225 REMARK 465 ALA A 226 REMARK 465 ASN A 227 REMARK 465 GLU A 228 REMARK 465 PRO A 244 REMARK 465 LYS A 245 REMARK 465 THR A 246 REMARK 465 GLU A 247 REMARK 465 THR A 248 REMARK 465 TYR A 249 REMARK 465 VAL A 250 REMARK 465 GLU A 251 REMARK 465 ALA A 252 REMARK 465 ASN A 253 REMARK 465 MET A 254 REMARK 465 GLY A 255 REMARK 465 LEU A 256 REMARK 465 ASN A 257 REMARK 465 PRO A 258 REMARK 465 SER A 259 REMARK 465 SER A 260 REMARK 465 PRO A 261 REMARK 465 ASN A 262 REMARK 465 HIS A 459 REMARK 465 GLN A 460 REMARK 465 MET A 461 REMARK 465 THR A 462 REMARK 465 LYS B 686 REMARK 465 SER B 697 REMARK 465 SER B 698 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue E8O A 501 DBREF 6LB6 A 224 462 UNP P19793 RXRA_HUMAN 224 462 DBREF 6LB6 B 686 698 UNP Q15596 NCOA2_HUMAN 686 698 SEQADV 6LB6 GLY A 220 UNP P19793 EXPRESSION TAG SEQADV 6LB6 SER A 221 UNP P19793 EXPRESSION TAG SEQADV 6LB6 SER A 222 UNP P19793 EXPRESSION TAG SEQADV 6LB6 HIS A 223 UNP P19793 EXPRESSION TAG SEQRES 1 A 243 GLY SER SER HIS SER SER ALA ASN GLU ASP MET PRO VAL SEQRES 2 A 243 GLU ARG ILE LEU GLU ALA GLU LEU ALA VAL GLU PRO LYS SEQRES 3 A 243 THR GLU THR TYR VAL GLU ALA ASN MET GLY LEU ASN PRO SEQRES 4 A 243 SER SER PRO ASN ASP PRO VAL THR ASN ILE CYS GLN ALA SEQRES 5 A 243 ALA ASP LYS GLN LEU PHE THR LEU VAL GLU TRP ALA LYS SEQRES 6 A 243 ARG ILE PRO HIS PHE SER GLU LEU PRO LEU ASP ASP GLN SEQRES 7 A 243 VAL ILE LEU LEU ARG ALA GLY TRP ASN GLU LEU LEU ILE SEQRES 8 A 243 ALA SER PHE SER HIS ARG SER ILE ALA VAL LYS ASP GLY SEQRES 9 A 243 ILE LEU LEU ALA THR GLY LEU HIS VAL HIS ARG ASN SER SEQRES 10 A 243 ALA HIS SER ALA GLY VAL GLY ALA ILE PHE ASP ARG VAL SEQRES 11 A 243 LEU THR GLU LEU VAL SER LYS MET ARG ASP MET GLN MET SEQRES 12 A 243 ASP LYS THR GLU LEU GLY CYS LEU ARG ALA ILE VAL LEU SEQRES 13 A 243 PHE ASN PRO ASP SER LYS GLY LEU SER ASN PRO ALA GLU SEQRES 14 A 243 VAL GLU ALA LEU ARG GLU LYS VAL TYR ALA SER LEU GLU SEQRES 15 A 243 ALA TYR CYS LYS HIS LYS TYR PRO GLU GLN PRO GLY ARG SEQRES 16 A 243 PHE ALA LYS LEU LEU LEU ARG LEU PRO ALA LEU ARG SER SEQRES 17 A 243 ILE GLY LEU LYS CYS LEU GLU HIS LEU PHE PHE PHE LYS SEQRES 18 A 243 LEU ILE GLY ASP THR PRO ILE ASP THR PHE LEU MET GLU SEQRES 19 A 243 MET LEU GLU ALA PRO HIS GLN MET THR SEQRES 1 B 13 LYS HIS LYS ILE LEU HIS ARG LEU LEU GLN ASP SER SER HET E8O A 501 26 HETNAM E8O 6-[ETHYL-[4-(2-METHYLPROPOXY)-3-PROPAN-2-YL- HETNAM 2 E8O PHENYL]AMINO]PYRIDINE-3-CARBOXYLIC ACID FORMUL 3 E8O C21 H28 N2 O3 FORMUL 4 HOH *51(H2 O) HELIX 1 AA1 PRO A 231 GLU A 243 1 13 HELIX 2 AA2 PRO A 264 ILE A 286 1 23 HELIX 3 AA3 PRO A 293 SER A 317 1 25 HELIX 4 AA4 ARG A 334 ALA A 340 1 7 HELIX 5 AA5 VAL A 342 LEU A 353 1 12 HELIX 6 AA6 LEU A 353 GLN A 361 1 9 HELIX 7 AA7 ASP A 363 PHE A 376 1 14 HELIX 8 AA8 ASN A 385 TYR A 408 1 24 HELIX 9 AA9 GLY A 413 LEU A 420 1 8 HELIX 10 AB1 ARG A 421 GLY A 443 1 23 HELIX 11 AB2 ASP A 448 LEU A 455 1 8 HELIX 12 AB3 LYS B 688 ASP B 696 1 9 SHEET 1 AA1 2 GLY A 323 LEU A 325 0 SHEET 2 AA1 2 HIS A 331 HIS A 333 -1 O VAL A 332 N ILE A 324 SITE 1 AC1 14 ILE A 268 ALA A 271 ALA A 272 GLN A 275 SITE 2 AC1 14 ASN A 306 LEU A 309 ILE A 310 PHE A 313 SITE 3 AC1 14 ARG A 316 LEU A 326 ALA A 327 VAL A 342 SITE 4 AC1 14 CYS A 432 PHE A 439 CRYST1 65.698 65.698 111.194 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 0.015221 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015221 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008993 0.00000