HEADER TRANSCRIPTION 14-MAR-11 3R29 TITLE CRYSTAL STRUCTURE OF RXRALPHA LIGAND-BINDING DOMAIN COMPLEXED WITH TITLE 2 COREPRESSOR SMRT2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOIC ACID RECEPTOR RXR-ALPHA; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: LIGAND BINDING DOMAIN (UNP RESIDUES 223-462); COMPND 5 SYNONYM: RETINOID X RECEPTOR ALPHA, NUCLEAR RECEPTOR SUBFAMILY 2 COMPND 6 GROUP B MEMBER 1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: NUCLEAR RECEPTOR COREPRESSOR 2; COMPND 10 CHAIN: C, D; COMPND 11 FRAGMENT: UNP RESIDUES 2346-2361; COMPND 12 SYNONYM: SMRT, N-COR2, CTG REPEAT PROTEIN 26, SMAP270, SILENCING COMPND 13 MEDIATOR OF RETINOIC ACID AND THYROID HORMONE RECEPTOR, T3 RECEPTOR- COMPND 14 ASSOCIATING FACTOR, TRAC, THYROID-RECEPTOR-ASSOCIATED COREPRESSOR, COMPND 15 RETINOIC-ACID-RECEPTOR-ASSOCIATED COREPRESSOR; COMPND 16 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; 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, TRANSCRIPTION FACTOR, LIGAND-BINDING DOMAIN, KEYWDS 2 TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR H.ZHANG,L.CHEN,J.CHEN,H.JIANG,X.SHEN REVDAT 3 27-JUL-11 3R29 1 JRNL REVDAT 2 08-JUN-11 3R29 1 JRNL REVDAT 1 25-MAY-11 3R29 0 JRNL AUTH H.ZHANG,L.CHEN,J.CHEN,H.JIANG,X.SHEN JRNL TITL STRUCTURAL BASIS FOR RETINOIC X RECEPTOR REPRESSION ON THE JRNL TITL 2 TETRAMER. JRNL REF J.BIOL.CHEM. V. 286 24593 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21613212 JRNL DOI 10.1074/JBC.M111.245498 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 12568 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 + TEST SET) : 0.244 REMARK 3 R VALUE (WORKING SET) : 0.240 REMARK 3 FREE R VALUE : 0.326 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 651 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 835 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2610 REMARK 3 BIN FREE R VALUE SET COUNT : 42 REMARK 3 BIN FREE R VALUE : 0.4590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3556 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 39 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.05000 REMARK 3 B22 (A**2) : -0.05000 REMARK 3 B33 (A**2) : 0.10000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.514 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.408 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 20.616 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.913 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.839 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3604 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4861 ; 1.814 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 443 ; 7.725 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 151 ;33.332 ;23.642 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 673 ;23.137 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;19.544 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 563 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2626 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1904 ; 0.293 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2468 ; 0.332 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 193 ; 0.195 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 73 ; 0.315 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.491 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2290 ; 0.736 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3598 ; 1.320 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1448 ; 1.707 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1263 ; 2.813 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3R29 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAR-11. REMARK 100 THE RCSB ID CODE IS RCSB064397. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JAN-11 REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9753 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13640 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 118.225 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 49.2000 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.44700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.300 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 3NSP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM CACODYLATE, 15% PEG4000, REMARK 280 100 MM MAGNESIUM ACETATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 42.01000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 59.11000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 59.11000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.00500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 59.11000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 59.11000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 63.01500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 59.11000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 59.11000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 21.00500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 59.11000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 59.11000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 63.01500 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 42.01000 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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 16680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -117.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D, C 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 42.01000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 30 LIES ON A SPECIAL POSITION. 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 THR A 223 REMARK 465 SER A 224 REMARK 465 SER A 225 REMARK 465 ALA A 226 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 GLU A 456 REMARK 465 ALA A 457 REMARK 465 PRO A 458 REMARK 465 HIS A 459 REMARK 465 GLN A 460 REMARK 465 MET A 461 REMARK 465 THR A 462 REMARK 465 THR B 223 REMARK 465 SER B 224 REMARK 465 SER B 225 REMARK 465 ALA B 226 REMARK 465 THR B 246 REMARK 465 GLU B 247 REMARK 465 THR B 248 REMARK 465 TYR B 249 REMARK 465 VAL B 250 REMARK 465 GLU B 251 REMARK 465 ALA B 252 REMARK 465 ASN B 253 REMARK 465 MET B 254 REMARK 465 GLY B 255 REMARK 465 LEU B 256 REMARK 465 ASN B 257 REMARK 465 PRO B 258 REMARK 465 SER B 259 REMARK 465 SER B 260 REMARK 465 PRO B 261 REMARK 465 ASN B 262 REMARK 465 GLU B 456 REMARK 465 ALA B 457 REMARK 465 PRO B 458 REMARK 465 HIS B 459 REMARK 465 GLN B 460 REMARK 465 MET B 461 REMARK 465 THR B 462 REMARK 465 THR D 2337 REMARK 465 ASN D 2338 REMARK 465 MET D 2339 REMARK 465 GLY D 2351 REMARK 465 LYS D 2352 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ALA B 283 CD1 PHE B 289 1.20 REMARK 500 O LEU A 441 OD2 ASP A 444 1.53 REMARK 500 CB ALA B 283 CE1 PHE B 289 1.76 REMARK 500 C ALA B 283 CD1 PHE B 289 1.78 REMARK 500 NH1 ARG B 334 OD2 ASP B 347 1.89 REMARK 500 O LYS C 2347 O LEU C 2349 1.91 REMARK 500 O PHE B 438 CD1 ILE B 442 1.91 REMARK 500 O ASN B 335 OG SER B 339 1.94 REMARK 500 C ALA B 283 CE1 PHE B 289 2.00 REMARK 500 O LEU B 292 NE2 GLN B 297 2.07 REMARK 500 REMARK 500 REMARK: NULL 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 NE2 HIS A 435 CD1 ILE A 442 8555 1.42 REMARK 500 CE MET B 452 O GLY C 2340 8555 1.79 REMARK 500 NH1 ARG B 234 NH1 ARG B 285 8554 1.95 REMARK 500 CE MET A 452 O GLY D 2340 8555 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 THR A 445 N - CA - C ANGL. DEV. = -20.4 DEGREES REMARK 500 PRO B 231 C - N - CD ANGL. DEV. = -15.9 DEGREES REMARK 500 GLN B 270 N - CA - C ANGL. DEV. = -18.9 DEGREES REMARK 500 MET C2339 N - CA - C ANGL. DEV. = 16.3 DEGREES REMARK 500 LEU C2349 N - CA - C ANGL. DEV. = -20.7 DEGREES 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 ASP A 229 43.74 -151.45 REMARK 500 MET A 230 63.46 -158.14 REMARK 500 HIS A 288 -1.73 80.45 REMARK 500 SER A 339 25.10 -73.11 REMARK 500 ALA A 340 -0.73 -144.76 REMARK 500 LEU A 353 -61.94 -131.33 REMARK 500 ASN A 385 80.65 -155.44 REMARK 500 HIS A 406 -73.86 -48.93 REMARK 500 GLN A 411 90.75 -69.02 REMARK 500 ASP A 444 -128.48 55.57 REMARK 500 THR A 445 -127.07 58.32 REMARK 500 MET A 452 44.31 76.42 REMARK 500 MET A 454 2.71 86.68 REMARK 500 GLU B 228 66.64 -110.76 REMARK 500 ALA B 271 1.67 87.64 REMARK 500 PHE B 277 -73.39 -53.56 REMARK 500 HIS B 288 -4.33 83.46 REMARK 500 GLN B 297 -33.70 -39.27 REMARK 500 VAL B 342 17.19 -147.48 REMARK 500 ASP B 359 -32.87 -37.11 REMARK 500 ALA B 387 -7.39 -55.41 REMARK 500 LEU C2341 -54.77 -123.98 REMARK 500 MET C2350 0.72 87.01 REMARK 500 LEU D2349 11.16 -67.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 MET C2339 23.3 L L OUTSIDE RANGE REMARK 500 LEU C2349 46.2 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3R2A RELATED DB: PDB DBREF 3R29 A 223 462 UNP P19793 RXRA_HUMAN 223 462 DBREF 3R29 B 223 462 UNP P19793 RXRA_HUMAN 223 462 DBREF 3R29 C 2337 2352 UNP Q9Y618 NCOR2_HUMAN 2346 2361 DBREF 3R29 D 2337 2352 UNP Q9Y618 NCOR2_HUMAN 2346 2361 SEQRES 1 A 240 THR SER SER ALA ASN GLU ASP MET PRO VAL GLU ARG ILE SEQRES 2 A 240 LEU GLU ALA GLU LEU ALA VAL GLU PRO LYS THR GLU THR SEQRES 3 A 240 TYR VAL GLU ALA ASN MET GLY LEU ASN PRO SER SER PRO SEQRES 4 A 240 ASN ASP PRO VAL THR ASN ILE CYS GLN ALA ALA ASP LYS SEQRES 5 A 240 GLN LEU PHE THR LEU VAL GLU TRP ALA LYS ARG ILE PRO SEQRES 6 A 240 HIS PHE SER GLU LEU PRO LEU ASP ASP GLN VAL ILE LEU SEQRES 7 A 240 LEU ARG ALA GLY TRP ASN GLU LEU LEU ILE ALA SER PHE SEQRES 8 A 240 SER HIS ARG SER ILE ALA VAL LYS ASP GLY ILE LEU LEU SEQRES 9 A 240 ALA THR GLY LEU HIS VAL HIS ARG ASN SER ALA HIS SER SEQRES 10 A 240 ALA GLY VAL GLY ALA ILE PHE ASP ARG VAL LEU THR GLU SEQRES 11 A 240 LEU VAL SER LYS MET ARG ASP MET GLN MET ASP LYS THR SEQRES 12 A 240 GLU LEU GLY CYS LEU ARG ALA ILE VAL LEU PHE ASN PRO SEQRES 13 A 240 ASP SER LYS GLY LEU SER ASN PRO ALA GLU VAL GLU ALA SEQRES 14 A 240 LEU ARG GLU LYS VAL TYR ALA SER LEU GLU ALA TYR CYS SEQRES 15 A 240 LYS HIS LYS TYR PRO GLU GLN PRO GLY ARG PHE ALA LYS SEQRES 16 A 240 LEU LEU LEU ARG LEU PRO ALA LEU ARG SER ILE GLY LEU SEQRES 17 A 240 LYS CYS LEU GLU HIS LEU PHE PHE PHE LYS LEU ILE GLY SEQRES 18 A 240 ASP THR PRO ILE ASP THR PHE LEU MET GLU MET LEU GLU SEQRES 19 A 240 ALA PRO HIS GLN MET THR SEQRES 1 B 240 THR SER SER ALA ASN GLU ASP MET PRO VAL GLU ARG ILE SEQRES 2 B 240 LEU GLU ALA GLU LEU ALA VAL GLU PRO LYS THR GLU THR SEQRES 3 B 240 TYR VAL GLU ALA ASN MET GLY LEU ASN PRO SER SER PRO SEQRES 4 B 240 ASN ASP PRO VAL THR ASN ILE CYS GLN ALA ALA ASP LYS SEQRES 5 B 240 GLN LEU PHE THR LEU VAL GLU TRP ALA LYS ARG ILE PRO SEQRES 6 B 240 HIS PHE SER GLU LEU PRO LEU ASP ASP GLN VAL ILE LEU SEQRES 7 B 240 LEU ARG ALA GLY TRP ASN GLU LEU LEU ILE ALA SER PHE SEQRES 8 B 240 SER HIS ARG SER ILE ALA VAL LYS ASP GLY ILE LEU LEU SEQRES 9 B 240 ALA THR GLY LEU HIS VAL HIS ARG ASN SER ALA HIS SER SEQRES 10 B 240 ALA GLY VAL GLY ALA ILE PHE ASP ARG VAL LEU THR GLU SEQRES 11 B 240 LEU VAL SER LYS MET ARG ASP MET GLN MET ASP LYS THR SEQRES 12 B 240 GLU LEU GLY CYS LEU ARG ALA ILE VAL LEU PHE ASN PRO SEQRES 13 B 240 ASP SER LYS GLY LEU SER ASN PRO ALA GLU VAL GLU ALA SEQRES 14 B 240 LEU ARG GLU LYS VAL TYR ALA SER LEU GLU ALA TYR CYS SEQRES 15 B 240 LYS HIS LYS TYR PRO GLU GLN PRO GLY ARG PHE ALA LYS SEQRES 16 B 240 LEU LEU LEU ARG LEU PRO ALA LEU ARG SER ILE GLY LEU SEQRES 17 B 240 LYS CYS LEU GLU HIS LEU PHE PHE PHE LYS LEU ILE GLY SEQRES 18 B 240 ASP THR PRO ILE ASP THR PHE LEU MET GLU MET LEU GLU SEQRES 19 B 240 ALA PRO HIS GLN MET THR SEQRES 1 C 16 THR ASN MET GLY LEU GLU ALA ILE ILE ARG LYS ALA LEU SEQRES 2 C 16 MET GLY LYS SEQRES 1 D 16 THR ASN MET GLY LEU GLU ALA ILE ILE ARG LYS ALA LEU SEQRES 2 D 16 MET GLY LYS FORMUL 5 HOH *39(H2 O) HELIX 1 1 PRO A 231 VAL A 242 1 12 HELIX 2 2 VAL A 265 GLN A 270 1 6 HELIX 3 3 ALA A 271 ARG A 285 1 15 HELIX 4 4 PRO A 293 SER A 317 1 25 HELIX 5 5 ARG A 334 SER A 339 1 6 HELIX 6 6 VAL A 342 LEU A 353 1 12 HELIX 7 7 LEU A 353 GLN A 361 1 9 HELIX 8 8 ASP A 363 PHE A 376 1 14 HELIX 9 9 ASN A 385 TYR A 408 1 24 HELIX 10 10 GLY A 413 ASP A 444 1 32 HELIX 11 11 VAL B 232 GLU B 243 1 12 HELIX 12 12 ASP B 263 CYS B 269 1 7 HELIX 13 13 ALA B 271 ARG B 285 1 15 HELIX 14 14 PRO B 293 ILE B 318 1 26 HELIX 15 15 ARG B 334 ALA B 340 1 7 HELIX 16 16 VAL B 342 LEU B 353 1 12 HELIX 17 17 LEU B 353 MET B 360 1 8 HELIX 18 18 ASP B 363 PHE B 376 1 14 HELIX 19 19 ASN B 385 TYR B 408 1 24 HELIX 20 20 GLY B 413 LEU B 420 1 8 HELIX 21 21 LEU B 420 ILE B 442 1 23 HELIX 22 22 THR B 449 GLU B 453 5 5 HELIX 23 23 LEU C 2341 LEU C 2349 1 9 HELIX 24 24 LEU D 2341 LEU D 2349 1 9 SHEET 1 A 2 GLY A 323 LEU A 325 0 SHEET 2 A 2 HIS A 331 HIS A 333 -1 O VAL A 332 N ILE A 324 SHEET 1 B 2 GLY B 323 LEU B 326 0 SHEET 2 B 2 LEU B 330 HIS B 333 -1 O VAL B 332 N ILE B 324 CRYST1 118.220 118.220 84.020 90.00 90.00 90.00 P 41 21 2 16 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 0.008459 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008459 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011902 0.00000 MASTER 456 0 0 24 4 0 0 6 0 0 0 42 END