HEADER TRANSCRIPTION 19-DEC-17 6FBQ TITLE CRYSTAL STRUCTURE OF THE HUMAN RETINOID X RECEPTOR DNA-BINDING DOMAIN TITLE 2 BOUND TO THE HUMAN MEP DR1 RESPONSE ELEMENT, PH 7.0 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 6FBQ 1 REMARK REVDAT 2 09-JAN-19 6FBQ 1 JRNL REVDAT 1 05-DEC-18 6FBQ 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. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.7 REMARK 3 NUMBER OF REFLECTIONS : 32765 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) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1658 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 : 16 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.65 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.19 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2905 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2140 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2773 REMARK 3 BIN R VALUE (WORKING SET) : 0.2140 REMARK 3 BIN FREE R VALUE : 0.2150 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.54 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 132 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 : 1315 REMARK 3 NUCLEIC ACID ATOMS : 691 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 430 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.07830 REMARK 3 B22 (A**2) : 1.13190 REMARK 3 B33 (A**2) : 0.94640 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.88590 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.190 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.110 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.103 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.117 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.093 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 : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 4371 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 7938 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 952 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 36 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 641 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 4371 ; 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 : 297 ; 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 : 5023 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.04 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.33 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 18.35 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): -24.8810 19.5641 25.9246 REMARK 3 T TENSOR REMARK 3 T11: -0.0361 T22: -0.0800 REMARK 3 T33: -0.0722 T12: -0.0206 REMARK 3 T13: -0.0053 T23: -0.0024 REMARK 3 L TENSOR REMARK 3 L11: 1.7146 L22: 2.9875 REMARK 3 L33: 2.0371 L12: 0.3464 REMARK 3 L13: 0.8961 L23: 1.0375 REMARK 3 S TENSOR REMARK 3 S11: -0.0732 S12: 0.1358 S13: 0.0391 REMARK 3 S21: 0.0439 S22: 0.1565 S23: -0.0929 REMARK 3 S31: -0.0927 S32: 0.2179 S33: -0.0833 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): -39.4789 -4.5538 9.7017 REMARK 3 T TENSOR REMARK 3 T11: 0.0042 T22: -0.1366 REMARK 3 T33: -0.1038 T12: -0.0316 REMARK 3 T13: -0.0332 T23: 0.0046 REMARK 3 L TENSOR REMARK 3 L11: 1.4418 L22: 3.5229 REMARK 3 L33: 5.6005 L12: 0.9634 REMARK 3 L13: 0.9825 L23: -0.9047 REMARK 3 S TENSOR REMARK 3 S11: 0.0288 S12: 0.1035 S13: -0.0627 REMARK 3 S21: -0.4435 S22: 0.1672 S23: 0.1966 REMARK 3 S31: 0.8455 S32: -0.0484 S33: -0.1960 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { C|* } REMARK 3 ORIGIN FOR THE GROUP (A): -25.8703 11.5735 12.1334 REMARK 3 T TENSOR REMARK 3 T11: -0.0554 T22: 0.0302 REMARK 3 T33: -0.0416 T12: -0.0622 REMARK 3 T13: 0.0259 T23: -0.0167 REMARK 3 L TENSOR REMARK 3 L11: 1.4903 L22: 1.6140 REMARK 3 L33: 1.8353 L12: 1.4413 REMARK 3 L13: 0.6674 L23: 1.6074 REMARK 3 S TENSOR REMARK 3 S11: -0.2589 S12: 0.3329 S13: -0.0325 REMARK 3 S21: -0.1714 S22: 0.3666 S23: -0.2118 REMARK 3 S31: -0.2641 S32: 0.4695 S33: -0.1077 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: { D|* } REMARK 3 ORIGIN FOR THE GROUP (A): -25.7932 9.2504 12.4575 REMARK 3 T TENSOR REMARK 3 T11: -0.0973 T22: 0.0375 REMARK 3 T33: -0.0496 T12: -0.0396 REMARK 3 T13: 0.0469 T23: -0.0535 REMARK 3 L TENSOR REMARK 3 L11: 1.1274 L22: 2.0464 REMARK 3 L33: 3.6622 L12: 1.0652 REMARK 3 L13: 2.2084 L23: 1.1795 REMARK 3 S TENSOR REMARK 3 S11: -0.1218 S12: 0.4284 S13: -0.2043 REMARK 3 S21: -0.1238 S22: 0.3895 S23: -0.2781 REMARK 3 S31: -0.1738 S32: 0.5649 S33: -0.2677 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6FBQ 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_1200008049. 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 : 7.0 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 : AIMLESS 0.5.25 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35888 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 REMARK 200 RESOLUTION RANGE LOW (A) : 42.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.8 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 65.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 1.07500 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: PHASER 2.6.0 REMARK 200 STARTING MODEL: 4CN5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.1M MOPS PH 7.0, 0.1M REMARK 280 NH4CL, 0.1M MGCL2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 51.66650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.12850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 51.66650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.12850 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 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 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 GLN A 210 REMARK 465 ARG A 211 REMARK 465 GLY A 212 REMARK 465 GLY B 126 REMARK 465 SER B 127 REMARK 465 HIS B 128 REMARK 465 MET B 129 REMARK 465 PHE B 130 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 B 211 CG CD NE CZ NH1 NH2 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 O2 DC C 1 H22 DG D 17 1.56 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. = 2.1 DEGREES REMARK 500 DG C 4 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG C 5 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA C 9 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC D 13 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC D 14 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 SER A 143 43.19 -98.04 REMARK 500 ASP A 173 -119.79 -105.11 REMARK 500 ASP A 176 38.18 -140.95 REMARK 500 ASP B 173 -124.27 -97.82 REMARK 500 ASP B 173 -124.27 -95.82 REMARK 500 ASP B 176 36.17 -145.36 REMARK 500 ASP B 176 39.64 -147.16 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 DT C 6 0.06 SIDE CHAIN REMARK 500 DT D 9 0.06 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 192 DISTANCE = 6.35 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 110.9 REMARK 620 3 CYS A 152 SG 116.7 106.0 REMARK 620 4 CYS A 155 SG 104.6 113.8 105.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 171 SG REMARK 620 2 CYS A 177 SG 104.5 REMARK 620 3 CYS A 187 SG 106.8 115.2 REMARK 620 4 CYS A 190 SG 111.8 111.7 106.8 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 116.7 105.2 REMARK 620 4 CYS B 155 SG 106.8 111.8 101.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 171 SG REMARK 620 2 CYS B 177 SG 101.5 REMARK 620 3 CYS B 187 SG 107.8 108.2 REMARK 620 4 CYS B 190 SG 114.9 117.9 106.1 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 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPO A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 302 DBREF 6FBQ A 130 212 UNP P19793 RXRA_HUMAN 33 115 DBREF 6FBQ B 130 212 UNP P19793 RXRA_HUMAN 33 115 DBREF 6FBQ C 1 17 PDB 6FBQ 6FBQ 1 17 DBREF 6FBQ D 1 17 PDB 6FBQ 6FBQ 1 17 SEQADV 6FBQ GLY A 126 UNP P19793 EXPRESSION TAG SEQADV 6FBQ SER A 127 UNP P19793 EXPRESSION TAG SEQADV 6FBQ HIS A 128 UNP P19793 EXPRESSION TAG SEQADV 6FBQ MET A 129 UNP P19793 EXPRESSION TAG SEQADV 6FBQ GLY B 126 UNP P19793 EXPRESSION TAG SEQADV 6FBQ SER B 127 UNP P19793 EXPRESSION TAG SEQADV 6FBQ HIS B 128 UNP P19793 EXPRESSION TAG SEQADV 6FBQ 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 A 302 1 HET MPO A 303 28 HET ZN B 301 1 HET ZN B 302 1 HETNAM ZN ZINC ION HETNAM MPO 3[N-MORPHOLINO]PROPANE SULFONIC ACID FORMUL 5 ZN 4(ZN 2+) FORMUL 7 MPO C7 H15 N O4 S FORMUL 10 HOH *430(H2 O) HELIX 1 AA1 CYS A 152 LYS A 165 1 14 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 LYS B 165 1 14 HELIX 5 AA5 GLN B 183 ARG B 186 5 4 HELIX 6 AA6 CYS B 187 MET B 198 1 12 HELIX 7 AA7 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 GLY B 144 HIS B 146 0 SHEET 2 AA3 2 VAL B 149 SER B 151 -1 O VAL B 149 N HIS B 146 LINK SG CYS A 135 ZN ZN A 301 1555 1555 2.36 LINK SG CYS A 138 ZN ZN A 301 1555 1555 2.33 LINK SG CYS A 152 ZN ZN A 301 1555 1555 2.29 LINK SG CYS A 155 ZN ZN A 301 1555 1555 2.38 LINK SG CYS A 171 ZN ZN A 302 1555 1555 2.41 LINK SG CYS A 177 ZN ZN A 302 1555 1555 2.34 LINK SG CYS A 187 ZN ZN A 302 1555 1555 2.33 LINK SG CYS A 190 ZN ZN A 302 1555 1555 2.33 LINK SG CYS B 135 ZN ZN B 301 1555 1555 2.32 LINK SG CYS B 138 ZN ZN B 301 1555 1555 2.30 LINK SG CYS B 152 ZN ZN B 301 1555 1555 2.37 LINK SG CYS B 155 ZN ZN B 301 1555 1555 2.36 LINK SG CYS B 171 ZN ZN B 302 1555 1555 2.38 LINK SG CYS B 177 ZN ZN B 302 1555 1555 2.35 LINK SG CYS B 187 ZN ZN B 302 1555 1555 2.43 LINK SG CYS B 190 ZN ZN B 302 1555 1555 2.23 SITE 1 AC1 4 CYS A 135 CYS A 138 CYS A 152 CYS A 155 SITE 1 AC2 4 CYS A 171 CYS A 177 CYS A 187 CYS A 190 SITE 1 AC3 19 ALA A 136 LYS A 145 VAL A 149 TYR A 150 SITE 2 AC3 19 ARG A 182 MET A 198 HOH A 413 HOH A 429 SITE 3 AC3 19 HOH A 461 HOH A 482 HOH A 485 ARG B 202 SITE 4 AC3 19 VAL B 205 GLN B 206 GLU B 207 HOH B 456 SITE 5 AC3 19 HOH B 458 HOH B 460 HOH B 496 SITE 1 AC4 4 CYS B 135 CYS B 138 CYS B 152 CYS B 155 SITE 1 AC5 4 CYS B 171 CYS B 177 CYS B 187 CYS B 190 CRYST1 103.333 44.257 62.137 90.00 98.31 90.00 C 1 2 1 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 0.009677 0.000000 0.001414 0.00000 SCALE2 0.000000 0.022595 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016264 0.00000