HEADER TRANSCRIPTION 21-JAN-03 1NQ7 TITLE CHARACTERIZATION OF LIGANDS FOR THE ORPHAN NUCLEAR RECEPTOR TITLE 2 RORBETA COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEAR RECEPTOR ROR-BETA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIGAND-BINDING DOMAIN; COMPND 5 SYNONYM: NUCLEAR RECEPTOR RZR-BETA; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: STEROID RECEPTOR COACTIVATOR-1; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: SECOND NR-BOX; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: NR1F2; 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: PET-15B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SOURCE 14 SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS SOURCE 15 (HUMAN). KEYWDS LIGAND-BINDING DOMAIN, RETINOIDS, RETINOIC ACID, SYNTHETIC KEYWDS 2 LIGAND, ANTAGONIST, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR C.STEHLIN-GAON,D.WILLMANN,S.SANGLIER,A.VAN DORSSELAER,J.- AUTHOR 2 P.RENAUD,D.MORAS,R.SCHUELE REVDAT 2 23-DEC-08 1NQ7 1 JRNL VERSN REVDAT 1 23-SEP-03 1NQ7 0 JRNL AUTH C.STEHLIN-GAON,D.WILLMANN,D.ZEYER,S.SANGLIER, JRNL AUTH 2 A.VAN DORSSELAER,J.-P.RENAUD,D.MORAS,R.SCHUELE JRNL TITL ALL-TRANS RETINOIC ACID IS A LIGAND FOR THE ORPHAN JRNL TITL 2 NUCLEAR RECEPTOR RORBETA JRNL REF NAT.STRUCT.BIOL. V. 10 820 2003 JRNL REFN ISSN 1072-8368 JRNL PMID 12958591 JRNL DOI 10.1038/NSB979 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.87 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) (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 52613 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) : 0.201 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2668 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 8038 REMARK 3 BIN R VALUE (WORKING SET) : 0.2220 REMARK 3 BIN FREE R VALUE : 0.2440 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 456 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.011 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2066 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 381 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.58000 REMARK 3 B22 (A**2) : 1.27000 REMARK 3 B33 (A**2) : -2.86000 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) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.07 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) : 0.20 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.10 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.10 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.73 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) : 1.630 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.270 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.160 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.850 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.30 REMARK 3 BSOL : 54.28 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ALRT.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ALRT.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NQ7 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JAN-03. REMARK 100 THE RCSB ID CODE IS RCSB018102. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-DEC-02 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0100 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52613 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 99.2 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06100 REMARK 200 FOR THE DATA SET : 32.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1K4W REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG6000, NACL, TRIS-HCL, CHAPS, REMARK 280 DTT, PH 8.0, VAPOR DIFFUSION, HANGING DROP, 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 26.41150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.83400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.17150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.83400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.41150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.17150 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: 2060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 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 TRP A 239 14.20 59.97 REMARK 500 SER A 335 50.18 -140.33 REMARK 500 TRP A 374 -5.11 74.69 REMARK 500 ASP A 403 3.02 -68.33 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 ARL A 800 DBREF 1NQ7 A 208 451 UNP P45446 RORB_RAT 208 451 DBREF 1NQ7 B 687 696 GB 1906028 AAB50242 687 696 SEQRES 1 A 244 THR MET SER GLU ILE ASP ARG ILE ALA GLN ASN ILE ILE SEQRES 2 A 244 LYS SER HIS LEU GLU THR CYS GLN TYR THR MET GLU GLU SEQRES 3 A 244 LEU HIS GLN LEU ALA TRP GLN THR HIS THR TYR GLU GLU SEQRES 4 A 244 ILE LYS ALA TYR GLN SER LYS SER ARG GLU ALA LEU TRP SEQRES 5 A 244 GLN GLN CYS ALA ILE GLN ILE THR HIS ALA ILE GLN TYR SEQRES 6 A 244 VAL VAL GLU PHE ALA LYS ARG ILE THR GLY PHE MET GLU SEQRES 7 A 244 LEU CYS GLN ASN ASP GLN ILE LEU LEU LEU LYS SER GLY SEQRES 8 A 244 CYS LEU GLU VAL VAL LEU VAL ARG MET CYS ARG ALA PHE SEQRES 9 A 244 ASN PRO LEU ASN ASN THR VAL LEU PHE GLU GLY LYS TYR SEQRES 10 A 244 GLY GLY MET GLN MET PHE LYS ALA LEU GLY SER ASP ASP SEQRES 11 A 244 LEU VAL ASN GLU ALA PHE ASP PHE ALA LYS ASN LEU CYS SEQRES 12 A 244 SER LEU GLN LEU THR GLU GLU GLU ILE ALA LEU PHE SER SEQRES 13 A 244 SER ALA VAL LEU ILE SER PRO ASP ARG ALA TRP LEU LEU SEQRES 14 A 244 GLU PRO ARG LYS VAL GLN LYS LEU GLN GLU LYS ILE TYR SEQRES 15 A 244 PHE ALA LEU GLN HIS VAL ILE GLN LYS ASN HIS LEU ASP SEQRES 16 A 244 ASP GLU THR LEU ALA LYS LEU ILE ALA LYS ILE PRO THR SEQRES 17 A 244 ILE THR ALA VAL CYS ASN LEU HIS GLY GLU LYS LEU GLN SEQRES 18 A 244 VAL PHE LYS GLN SER HIS PRO ASP ILE VAL ASN THR LEU SEQRES 19 A 244 PHE PRO PRO LEU TYR LYS GLU LEU PHE ASN SEQRES 1 B 10 HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU HET ARL A 800 25 HETNAM ARL 7-(3,5-DITERT-BUTYLPHENYL)-3-METHYLOCTA-2,4,6- HETNAM 2 ARL TRIENOIC ACID FORMUL 3 ARL C23 H32 O2 FORMUL 4 HOH *373(H2 O) HELIX 1 1 THR A 208 CYS A 227 1 20 HELIX 2 2 THR A 230 ALA A 238 1 9 HELIX 3 3 THR A 243 LYS A 253 1 11 HELIX 4 4 SER A 254 ARG A 279 1 26 HELIX 5 5 ILE A 280 GLU A 285 1 6 HELIX 6 6 CYS A 287 CYS A 308 1 22 HELIX 7 7 GLN A 328 GLY A 334 5 7 HELIX 8 8 SER A 335 SER A 351 1 17 HELIX 9 9 THR A 355 ILE A 368 1 14 HELIX 10 10 GLU A 377 HIS A 400 1 24 HELIX 11 11 GLU A 404 LYS A 412 1 9 HELIX 12 12 LYS A 412 HIS A 434 1 23 HELIX 13 13 HIS A 434 LEU A 441 1 8 HELIX 14 14 PRO A 443 ASN A 451 1 9 HELIX 15 15 HIS B 687 GLU B 696 1 10 SHEET 1 A 3 PHE A 311 ASN A 312 0 SHEET 2 A 3 THR A 317 PHE A 320 -1 O THR A 317 N ASN A 312 SHEET 3 A 3 LYS A 323 GLY A 326 -1 O LYS A 323 N PHE A 320 SITE 1 AC1 11 CYS A 227 GLN A 228 TYR A 229 CYS A 262 SITE 2 AC1 11 LEU A 300 ARG A 306 MET A 307 LEU A 319 SITE 3 AC1 11 PHE A 330 HOH A1006 HOH A1007 CRYST1 52.823 58.343 105.668 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 0.018931 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017140 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009464 0.00000