HEADER TRANSCRIPTION 19-DEC-17 6FBR TITLE CRYSTAL STRUCTURE OF THE HUMAN RETINOID X RECEPTOR DNA-BINDING DOMAIN TITLE 2 BOUND TO THE HUMAN MEP DR1 RESPONSE ELEMENT, PH 4.2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOIC ACID RECEPTOR RXR-ALPHA; COMPND 3 CHAIN: A, B; 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: DNA (5'- COMPND 9 D(*CP*TP*GP*GP*GP*TP*CP*AP*AP*AP*GP*TP*TP*CP*AP*TP*C)-3'); COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'- COMPND 14 D(*GP*AP*TP*GP*AP*AP*CP*TP*TP*TP*GP*AP*CP*CP*CP*AP*G)-3'); COMPND 15 CHAIN: D; 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS TRANSCRIPTION-DNA COMPLEX, NUCLEAR RECEPTOR, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR A.G.MCEWEN,P.POUSSIN-COURMONTAGNE,J.OSZ,N.ROCHEL REVDAT 3 17-JAN-24 6FBR 1 REMARK REVDAT 2 09-JAN-19 6FBR 1 JRNL REVDAT 1 05-DEC-18 6FBR 0 JRNL AUTH J.OSZ,A.G.MCEWEN,J.WOLF,P.POUSSIN-COURMONTAGNE, JRNL AUTH 2 C.PELUSO-ILTIS,Y.CHEBARO,B.KIEFFER,N.ROCHEL JRNL TITL MODULATION OF RXR-DNA COMPLEX ASSEMBLY BY DNA CONTEXT. JRNL REF MOL. CELL. ENDOCRINOL. V. 481 44 2019 JRNL REFN ISSN 1872-8057 JRNL PMID 30476562 JRNL DOI 10.1016/J.MCE.2018.11.008 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 17378 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 869 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.000 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 9 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.23 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.71 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2418 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2360 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2297 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE : 0.2680 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 121 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1284 REMARK 3 NUCLEIC ACID ATOMS : 691 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 134 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.94 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.74380 REMARK 3 B22 (A**2) : -5.74380 REMARK 3 B33 (A**2) : 11.48770 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) : 0.300 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.212 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.182 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.187 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.172 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2128 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 2977 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 698 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 27 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 235 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2128 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 265 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 2261 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.06 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.90 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 20.49 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): -23.1899 24.5421 9.9389 REMARK 3 T TENSOR REMARK 3 T11: -0.0873 T22: -0.0713 REMARK 3 T33: -0.1494 T12: -0.0427 REMARK 3 T13: -0.0273 T23: 0.0486 REMARK 3 L TENSOR REMARK 3 L11: 5.1928 L22: 2.6856 REMARK 3 L33: 5.6509 L12: -1.1421 REMARK 3 L13: 0.2823 L23: -0.5133 REMARK 3 S TENSOR REMARK 3 S11: -0.0733 S12: -0.1299 S13: 0.2834 REMARK 3 S21: -0.0120 S22: 0.1264 S23: 0.0826 REMARK 3 S31: -0.4429 S32: -0.0720 S33: -0.0531 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): -19.5534 6.6159 35.6569 REMARK 3 T TENSOR REMARK 3 T11: -0.0501 T22: -0.0516 REMARK 3 T33: -0.1726 T12: 0.0057 REMARK 3 T13: -0.0081 T23: -0.0079 REMARK 3 L TENSOR REMARK 3 L11: 2.1898 L22: 4.8217 REMARK 3 L33: 4.7761 L12: 1.0478 REMARK 3 L13: -0.1823 L23: -1.6800 REMARK 3 S TENSOR REMARK 3 S11: 0.0111 S12: -0.0186 S13: -0.1991 REMARK 3 S21: 0.3368 S22: -0.0409 S23: -0.2518 REMARK 3 S31: 0.0660 S32: 0.3477 S33: 0.0297 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { C|* } REMARK 3 ORIGIN FOR THE GROUP (A): -29.5839 13.6507 21.0803 REMARK 3 T TENSOR REMARK 3 T11: 0.0154 T22: 0.0446 REMARK 3 T33: -0.2027 T12: -0.0563 REMARK 3 T13: 0.0013 T23: -0.0301 REMARK 3 L TENSOR REMARK 3 L11: 0.7889 L22: 0.8066 REMARK 3 L33: 2.7743 L12: 0.3565 REMARK 3 L13: 0.9435 L23: -2.3544 REMARK 3 S TENSOR REMARK 3 S11: 0.0448 S12: 0.0858 S13: 0.0792 REMARK 3 S21: -0.1693 S22: 0.1629 S23: 0.0005 REMARK 3 S31: 0.1180 S32: -0.3866 S33: -0.2077 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: { D|* } REMARK 3 ORIGIN FOR THE GROUP (A): -28.4779 11.9154 21.6350 REMARK 3 T TENSOR REMARK 3 T11: -0.0178 T22: 0.0351 REMARK 3 T33: -0.1736 T12: -0.0524 REMARK 3 T13: -0.0125 T23: -0.0248 REMARK 3 L TENSOR REMARK 3 L11: 0.7337 L22: 1.0818 REMARK 3 L33: 4.5951 L12: -0.1639 REMARK 3 L13: 0.6438 L23: -1.1800 REMARK 3 S TENSOR REMARK 3 S11: 0.0715 S12: 0.0169 S13: 0.0409 REMARK 3 S21: 0.0276 S22: 0.0389 S23: 0.0348 REMARK 3 S31: 0.3370 S32: -0.2017 S33: -0.1104 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6FBR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1200008052. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID30B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2821 REMARK 200 MONOCHROMATOR : SI(111) 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19015 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 46.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.2 REMARK 200 DATA REDUNDANCY : 4.624 REMARK 200 R MERGE (I) : 0.11300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 58.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.18 REMARK 200 R MERGE FOR SHELL (I) : 3.28000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.390 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: 6FBQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% PEG 300, 0.1M SODIUM PHOSPHATE REMARK 280 CITRATE PH 4.2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.37700 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 110.75400 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 110.75400 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 55.37700 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: 6600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 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 O2 PEG B 304 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 GLY A 126 REMARK 465 SER A 127 REMARK 465 HIS A 128 REMARK 465 MET A 129 REMARK 465 PHE A 130 REMARK 465 ARG A 209 REMARK 465 GLN A 210 REMARK 465 ARG A 211 REMARK 465 GLY A 212 REMARK 465 ASP B 173 REMARK 465 ASN B 174 REMARK 465 LYS B 175 REMARK 465 ASP B 176 REMARK 465 ARG B 211 REMARK 465 GLY B 212 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 172 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 208 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DG C 5 O3' DG C 5 C3' -0.042 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 DC C 1 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT C 2 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG C 3 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG C 4 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA C 9 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC D 7 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC D 15 O4' - C1' - N1 ANGL. DEV. = 2.7 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 ARG A 172 -103.16 16.08 REMARK 500 LYS A 175 -116.03 39.94 REMARK 500 CYS A 177 48.21 -76.35 REMARK 500 CYS B 171 -49.50 -0.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DG C 3 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH D 142 DISTANCE = 6.22 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 135 SG REMARK 620 2 CYS A 138 SG 110.0 REMARK 620 3 CYS A 152 SG 114.0 107.0 REMARK 620 4 CYS A 155 SG 106.3 114.4 105.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 135 SG REMARK 620 2 CYS B 138 SG 113.9 REMARK 620 3 CYS B 152 SG 117.5 103.9 REMARK 620 4 CYS B 155 SG 106.9 113.5 100.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 305 DBREF 6FBR A 130 212 UNP P19793 RXRA_HUMAN 33 115 DBREF 6FBR B 130 212 UNP P19793 RXRA_HUMAN 33 115 DBREF 6FBR C 1 17 PDB 6FBR 6FBR 1 17 DBREF 6FBR D 1 17 PDB 6FBR 6FBR 1 17 SEQADV 6FBR GLY A 126 UNP P19793 EXPRESSION TAG SEQADV 6FBR SER A 127 UNP P19793 EXPRESSION TAG SEQADV 6FBR HIS A 128 UNP P19793 EXPRESSION TAG SEQADV 6FBR MET A 129 UNP P19793 EXPRESSION TAG SEQADV 6FBR GLY B 126 UNP P19793 EXPRESSION TAG SEQADV 6FBR SER B 127 UNP P19793 EXPRESSION TAG SEQADV 6FBR HIS B 128 UNP P19793 EXPRESSION TAG SEQADV 6FBR MET B 129 UNP P19793 EXPRESSION TAG SEQRES 1 A 87 GLY SER HIS MET PHE THR LYS HIS ILE CYS ALA ILE CYS SEQRES 2 A 87 GLY ASP ARG SER SER GLY LYS HIS TYR GLY VAL TYR SER SEQRES 3 A 87 CYS GLU GLY CYS LYS GLY PHE PHE LYS ARG THR VAL ARG SEQRES 4 A 87 LYS ASP LEU THR TYR THR CYS ARG ASP ASN LYS ASP CYS SEQRES 5 A 87 LEU ILE ASP LYS ARG GLN ARG ASN ARG CYS GLN TYR CYS SEQRES 6 A 87 ARG TYR GLN LYS CYS LEU ALA MET GLY MET LYS ARG GLU SEQRES 7 A 87 ALA VAL GLN GLU GLU ARG GLN ARG GLY SEQRES 1 B 87 GLY SER HIS MET PHE THR LYS HIS ILE CYS ALA ILE CYS SEQRES 2 B 87 GLY ASP ARG SER SER GLY LYS HIS TYR GLY VAL TYR SER SEQRES 3 B 87 CYS GLU GLY CYS LYS GLY PHE PHE LYS ARG THR VAL ARG SEQRES 4 B 87 LYS ASP LEU THR TYR THR CYS ARG ASP ASN LYS ASP CYS SEQRES 5 B 87 LEU ILE ASP LYS ARG GLN ARG ASN ARG CYS GLN TYR CYS SEQRES 6 B 87 ARG TYR GLN LYS CYS LEU ALA MET GLY MET LYS ARG GLU SEQRES 7 B 87 ALA VAL GLN GLU GLU ARG GLN ARG GLY SEQRES 1 C 17 DC DT DG DG DG DT DC DA DA DA DG DT DT SEQRES 2 C 17 DC DA DT DC SEQRES 1 D 17 DG DA DT DG DA DA DC DT DT DT DG DA DC SEQRES 2 D 17 DC DC DA DG HET ZN A 301 1 HET ZN B 301 1 HET PO4 B 302 5 HET PGE B 303 10 HET PEG B 304 7 HET PEG B 305 7 HETNAM ZN ZINC ION HETNAM PO4 PHOSPHATE ION HETNAM PGE TRIETHYLENE GLYCOL HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 5 ZN 2(ZN 2+) FORMUL 7 PO4 O4 P 3- FORMUL 8 PGE C6 H14 O4 FORMUL 9 PEG 2(C4 H10 O3) FORMUL 11 HOH *134(H2 O) HELIX 1 AA1 CYS A 152 ASP A 166 1 15 HELIX 2 AA2 CYS A 187 GLY A 199 1 13 HELIX 3 AA3 LYS A 201 VAL A 205 5 5 HELIX 4 AA4 CYS B 152 ASP B 166 1 15 HELIX 5 AA5 CYS B 187 GLY B 199 1 13 HELIX 6 AA6 LYS B 201 VAL B 205 5 5 SHEET 1 AA1 2 HIS A 133 ILE A 134 0 SHEET 2 AA1 2 ARG A 141 SER A 142 -1 O SER A 142 N HIS A 133 SHEET 1 AA2 2 GLY A 144 HIS A 146 0 SHEET 2 AA2 2 VAL A 149 SER A 151 -1 O VAL A 149 N HIS A 146 SHEET 1 AA3 2 HIS B 133 ILE B 134 0 SHEET 2 AA3 2 ARG B 141 SER B 142 -1 O SER B 142 N HIS B 133 SHEET 1 AA4 2 LYS B 145 HIS B 146 0 SHEET 2 AA4 2 VAL B 149 TYR B 150 -1 O VAL B 149 N HIS B 146 SSBOND 1 CYS A 171 CYS A 187 1555 1555 2.05 SSBOND 2 CYS A 177 CYS A 190 1555 1555 2.05 LINK SG CYS A 135 ZN ZN A 301 1555 1555 2.38 LINK SG CYS A 138 ZN ZN A 301 1555 1555 2.39 LINK SG CYS A 152 ZN ZN A 301 1555 1555 2.26 LINK SG CYS A 155 ZN ZN A 301 1555 1555 2.33 LINK SG CYS B 135 ZN ZN B 301 1555 1555 2.35 LINK SG CYS B 138 ZN ZN B 301 1555 1555 2.30 LINK SG CYS B 152 ZN ZN B 301 1555 1555 2.39 LINK SG CYS B 155 ZN ZN B 301 1555 1555 2.37 SITE 1 AC1 4 CYS A 135 CYS A 138 CYS A 152 CYS A 155 SITE 1 AC2 4 CYS B 135 CYS B 138 CYS B 152 CYS B 155 SITE 1 AC3 7 LYS B 160 ARG B 161 LYS B 165 HOH B 403 SITE 2 AC3 7 HOH B 407 DC C 14 DG D 4 SITE 1 AC4 4 ARG B 202 GLU B 203 VAL B 205 GLU B 207 SITE 1 AC5 2 ARG B 202 GLU B 203 SITE 1 AC6 3 LYS B 201 ALA B 204 DA C 10 CRYST1 55.659 55.659 166.131 90.00 90.00 120.00 P 31 2 1 12 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 0.017967 0.010373 0.000000 0.00000 SCALE2 0.000000 0.020746 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006019 0.00000