HEADER TRANSCRIPTION/DNA 29-NOV-00 1GA5 TITLE CRYSTAL STRUCTURE OF THE ORPHAN NUCLEAR RECEPTOR REV-ERB(ALPHA) DNA- TITLE 2 BINDING DOMAIN BOUND TO ITS COGNATE RESPONSE ELEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*CP*TP*AP*GP*GP*TP*CP COMPND 3 *AP*G)-3'; COMPND 4 CHAIN: C, G; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*CP*TP*GP*AP*CP*CP*TP*AP*GP*TP*GP*AP*CP*CP*TP*AP*GP*TP COMPND 8 *(5IT)P*G)-3'; COMPND 9 CHAIN: D, H; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: ORPHAN NUCLEAR RECEPTOR NR1D1; COMPND 13 CHAIN: A, B, E, F; COMPND 14 FRAGMENT: DNA-BINDING DOMAIN PLUS C-TERMINAL EXTENSION; COMPND 15 SYNONYM: REV-ERB(ALPHA); COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHESIZED OPTIMAL DR2 TARGET; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: SYNTHESIZED OPTIMAL DR2 TARGET COMPLEMENTARY STRAND SOURCE 7 WITH 5-IODO-THYMIDINE; SOURCE 8 MOL_ID: 3; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: NR1D1 OR THRAL OR EAR1 OR HREV; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 15 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 16 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 17 EXPRESSION_SYSTEM_PLASMID: PGEX KEYWDS ORPHAN RECEPTOR, NUCLEAR RECEPTOR, DNA-BINDING, REVERB, REV-ERB, KEYWDS 2 TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.L.SIERK,Q.ZHAO,F.RASTINEJAD REVDAT 4 09-AUG-23 1GA5 1 REMARK SEQADV LINK REVDAT 3 04-OCT-17 1GA5 1 REMARK REVDAT 2 24-FEB-09 1GA5 1 VERSN REVDAT 1 16-NOV-01 1GA5 0 JRNL AUTH M.L.SIERK,Q.ZHAO,F.RASTINEJAD JRNL TITL DNA DEFORMABILITY AS A RECOGNITION FEATURE IN THE REVERB JRNL TITL 2 RESPONSE ELEMENT JRNL REF BIOCHEMISTRY V. 40 12833 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11669620 JRNL DOI 10.1021/BI011086R REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Q.ZHAO,S.KHORASANIZADEH,Y.MIYOSHI,M.LAZAR,F.RASTINEJAD REMARK 1 TITL STRUCTURAL ELEMENTS OF AN ORPHAN NUCLEAR RECEPTOR-DNA REMARK 1 TITL 2 COMPLEX REMARK 1 REF MOL.CELL V. 1 849 1998 REMARK 1 REFN ISSN 1097-2765 REMARK 1 DOI 10.1016/S1097-2765(00)80084-2 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 818521.390 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 75.0 REMARK 3 NUMBER OF REFLECTIONS : 19630 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) : 0.253 REMARK 3 FREE R VALUE : 0.299 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1940 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.49 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 63.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2640 REMARK 3 BIN R VALUE (WORKING SET) : 0.3895 REMARK 3 BIN FREE R VALUE : 0.4156 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 165 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.026 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2363 REMARK 3 NUCLEIC ACID ATOMS : 1628 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 279 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 30.65000 REMARK 3 B22 (A**2) : -17.89000 REMARK 3 B33 (A**2) : -12.77000 REMARK 3 B12 (A**2) : 7.40000 REMARK 3 B13 (A**2) : -2.34000 REMARK 3 B23 (A**2) : -4.41000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.41 REMARK 3 ESD FROM SIGMAA (A) : 0.58 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) : 0.51 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.62 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.030 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) : 2.920 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.630 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.330 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.710 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.27 REMARK 3 BSOL : 42.65 REMARK 3 REMARK 3 NCS MODEL : CONSTR 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 : DNA-RNA_REP_1.0.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ZINC.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA_1.0.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ZINC.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NCS RESTRAINTS USED UNTIL FINAL ROUND REMARK 3 OF REFINEMENT REMARK 4 REMARK 4 1GA5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-DEC-00. REMARK 100 THE DEPOSITION ID IS D_1000012424. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9054 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL GERMANIUM REMARK 200 TRIANGULAR MONOCHROMATOR REMARK 200 OPTICS : SEGMENTED MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25370 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 19.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 75.0 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 0.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.39300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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 1A6Y, RESIDUES 132-198 FROM CHAIN A & B, REMARK 200 PLUS DNA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG8000, 5MM MGCL2, 400 MM NACL, REMARK 280 TRIS, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 APPLY THE FOLLOWING TO CHAINS: C, D, 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, H, E, F 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 THR A -8 REMARK 465 LYS A -7 REMARK 465 LEU A -6 REMARK 465 ASN A -5 REMARK 465 GLY A -4 REMARK 465 MET A -3 REMARK 465 ARG A 79 REMARK 465 GLU A 80 REMARK 465 LYS A 81 REMARK 465 GLN A 82 REMARK 465 ARG A 83 REMARK 465 MET A 84 REMARK 465 THR B -8 REMARK 465 LYS B -7 REMARK 465 LEU B -6 REMARK 465 ASN B -5 REMARK 465 GLY B -4 REMARK 465 MET B -3 REMARK 465 ILE B 76 REMARK 465 PRO B 77 REMARK 465 LYS B 78 REMARK 465 ARG B 79 REMARK 465 GLU B 80 REMARK 465 LYS B 81 REMARK 465 GLN B 82 REMARK 465 ARG B 83 REMARK 465 MET B 84 REMARK 465 THR E -8 REMARK 465 LYS E -7 REMARK 465 LEU E -6 REMARK 465 ASN E -5 REMARK 465 GLY E -4 REMARK 465 MET E -3 REMARK 465 LYS E 78 REMARK 465 ARG E 79 REMARK 465 GLU E 80 REMARK 465 LYS E 81 REMARK 465 GLN E 82 REMARK 465 ARG E 83 REMARK 465 MET E 84 REMARK 465 THR F -8 REMARK 465 LYS F -7 REMARK 465 LEU F -6 REMARK 465 ASN F -5 REMARK 465 GLY F -4 REMARK 465 MET F -3 REMARK 465 ARG F 75 REMARK 465 ILE F 76 REMARK 465 PRO F 77 REMARK 465 LYS F 78 REMARK 465 ARG F 79 REMARK 465 GLU F 80 REMARK 465 LYS F 81 REMARK 465 GLN F 82 REMARK 465 ARG F 83 REMARK 465 MET F 84 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 LYS A 2 CG CD CE NZ REMARK 470 GLN A 30 CG CD OE1 NE2 REMARK 470 GLN A 31 CG CD OE1 NE2 REMARK 470 ASN A 32 CG OD1 ND2 REMARK 470 ILE A 33 CG1 CG2 CD1 REMARK 470 GLN A 33A CG CD OE1 NE2 REMARK 470 ARG A 36 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 40 CG OD1 ND2 REMARK 470 GLU A 41 CG CD OE1 OE2 REMARK 470 ARG A 52 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 55 CG CD OE1 NE2 REMARK 470 LYS A 59 CG CD CE NZ REMARK 470 VAL B -2 CG1 CG2 REMARK 470 GLN B 30 CG CD OE1 NE2 REMARK 470 GLN B 31 CG CD OE1 NE2 REMARK 470 ASN B 32 CG OD1 ND2 REMARK 470 GLN B 33A CG CD OE1 NE2 REMARK 470 ARG B 36 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 39 CG CD CE NZ REMARK 470 ASN B 40 CG OD1 ND2 REMARK 470 ASN B 42 CG OD1 ND2 REMARK 470 ARG B 47 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 55 CG CD OE1 NE2 REMARK 470 GLN E 31 CG CD OE1 NE2 REMARK 470 ASN E 32 CG OD1 ND2 REMARK 470 ARG E 36 CG CD NE CZ NH1 NH2 REMARK 470 LYS E 39 CG CD CE NZ REMARK 470 ASN E 40 CG OD1 ND2 REMARK 470 GLU E 41 CG CD OE1 OE2 REMARK 470 ASN E 42 CG OD1 ND2 REMARK 470 ARG E 52 CG CD NE CZ NH1 NH2 REMARK 470 LYS E 59 CG CD CE NZ REMARK 470 VAL F -2 CG1 CG2 REMARK 470 LEU F -1 CG CD1 CD2 REMARK 470 GLN F 30 CG CD OE1 NE2 REMARK 470 GLN F 31 CG CD OE1 NE2 REMARK 470 ASN F 32 CG OD1 ND2 REMARK 470 ILE F 33 CG1 CG2 CD1 REMARK 470 GLN F 33A CG CD OE1 NE2 REMARK 470 LYS F 35 CG CD CE NZ REMARK 470 ARG F 36 CG CD NE CZ NH1 NH2 REMARK 470 ASN F 42 CG OD1 ND2 REMARK 470 ARG F 68 CG CD NE CZ NH1 NH2 REMARK 470 ARG F 72 CG CD NE CZ NH1 NH2 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 6 -178.99 -61.47 REMARK 500 GLN A 30 107.78 164.16 REMARK 500 GLN A 31 17.85 94.02 REMARK 500 ASN A 32 148.67 -24.15 REMARK 500 ILE A 33 153.21 178.04 REMARK 500 LYS A 35 157.82 -44.23 REMARK 500 LYS A 39 -138.44 -152.70 REMARK 500 GLU A 41 15.13 -57.75 REMARK 500 ARG A 47 -36.92 -34.66 REMARK 500 PRO A 77 -96.38 -78.08 REMARK 500 ILE B 33 93.83 -45.69 REMARK 500 GLU B 41 39.88 20.31 REMARK 500 SER E 28 -91.04 -58.43 REMARK 500 GLN E 31 136.03 148.04 REMARK 500 ASN E 32 75.05 -62.28 REMARK 500 LEU E 38 43.58 -104.18 REMARK 500 LYS E 39 -155.12 178.27 REMARK 500 ASN E 42 46.47 -151.30 REMARK 500 LEU F -1 107.99 67.51 REMARK 500 ILE F 33 102.08 -41.23 REMARK 500 LYS F 35 156.32 -47.26 REMARK 500 LYS F 39 74.83 -150.64 REMARK 500 ASN F 40 54.71 33.68 REMARK 500 GLU F 41 38.34 23.91 REMARK 500 ASP F 69 30.20 -86.85 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 DC C 611 0.07 SIDE CHAIN REMARK 500 DC G 611 0.08 SIDE CHAIN REMARK 500 DG H 629 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL 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 450 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 1 SG REMARK 620 2 CYS A 4 SG 127.4 REMARK 620 3 CYS A 18 SG 103.4 103.1 REMARK 620 4 CYS A 21 SG 111.0 113.2 90.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 451 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 37 SG REMARK 620 2 CYS A 43 SG 97.4 REMARK 620 3 CYS A 53 SG 122.3 121.2 REMARK 620 4 CYS A 56 SG 87.3 98.1 122.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 550 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 1 SG REMARK 620 2 CYS B 4 SG 109.0 REMARK 620 3 CYS B 18 SG 121.0 110.4 REMARK 620 4 CYS B 21 SG 109.3 104.4 101.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 551 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 37 SG REMARK 620 2 CYS B 43 SG 99.5 REMARK 620 3 CYS B 53 SG 103.6 117.5 REMARK 620 4 CYS B 56 SG 124.4 106.4 106.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN E 450 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS E 1 SG REMARK 620 2 CYS E 4 SG 114.1 REMARK 620 3 CYS E 18 SG 119.0 109.6 REMARK 620 4 CYS E 21 SG 98.6 114.1 100.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN E 451 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS E 37 SG REMARK 620 2 CYS E 43 SG 98.9 REMARK 620 3 CYS E 53 SG 110.1 111.4 REMARK 620 4 CYS E 56 SG 111.6 104.2 118.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN F 550 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS F 1 SG REMARK 620 2 CYS F 4 SG 115.8 REMARK 620 3 CYS F 18 SG 115.0 109.0 REMARK 620 4 CYS F 21 SG 106.6 102.8 106.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN F 551 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS F 37 SG REMARK 620 2 CYS F 43 SG 108.9 REMARK 620 3 CYS F 53 SG 97.7 120.4 REMARK 620 4 CYS F 56 SG 109.6 120.4 97.0 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 450 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 451 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 550 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 551 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN E 450 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN E 451 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN F 550 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN F 551 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1A6Y RELATED DB: PDB REMARK 900 REV-ERB(ALPHA) DBD BOUND TO DNA, CRYSTAL FORM I REMARK 900 RELATED ID: 1HLZ RELATED DB: PDB REMARK 900 REV-ERB(ALPHA) DBD BOUND TO DNA, CRYSTAL FORM III DBREF 1GA5 A -8 84 UNP P20393 NR1D1_HUMAN 123 216 DBREF 1GA5 B -8 84 UNP P20393 NR1D1_HUMAN 123 216 DBREF 1GA5 E -8 84 UNP P20393 NR1D1_HUMAN 123 216 DBREF 1GA5 F -8 84 UNP P20393 NR1D1_HUMAN 123 216 DBREF 1GA5 C 600 619 PDB 1GA5 1GA5 600 619 DBREF 1GA5 D 621 640 PDB 1GA5 1GA5 621 640 DBREF 1GA5 G 600 619 PDB 1GA5 1GA5 600 619 DBREF 1GA5 H 621 640 PDB 1GA5 1GA5 621 640 SEQADV 1GA5 LEU A 16 UNP P20393 HIS 147 CLONING ARTIFACT SEQADV 1GA5 LEU B 16 UNP P20393 HIS 147 CLONING ARTIFACT SEQADV 1GA5 LEU E 16 UNP P20393 HIS 147 CLONING ARTIFACT SEQADV 1GA5 LEU F 16 UNP P20393 HIS 147 CLONING ARTIFACT SEQRES 1 C 20 DC DA DA DC DT DA DG DG DT DC DA DC DT SEQRES 2 C 20 DA DG DG DT DC DA DG SEQRES 1 D 20 DC DT DG DA DC DC DT DA DG DT DG DA DC SEQRES 2 D 20 DC DT DA DG DT 5IU DG SEQRES 1 G 20 DC DA DA DC DT DA DG DG DT DC DA DC DT SEQRES 2 G 20 DA DG DG DT DC DA DG SEQRES 1 H 20 DC DT DG DA DC DC DT DA DG DT DG DA DC SEQRES 2 H 20 DC DT DA DG DT 5IU DG SEQRES 1 A 94 THR LYS LEU ASN GLY MET VAL LEU LEU CYS LYS VAL CYS SEQRES 2 A 94 GLY ASP VAL ALA SER GLY PHE HIS TYR GLY VAL LEU ALA SEQRES 3 A 94 CYS GLU GLY CYS LYS GLY PHE PHE ARG ARG SER ILE GLN SEQRES 4 A 94 GLN ASN ILE GLN TYR LYS ARG CYS LEU LYS ASN GLU ASN SEQRES 5 A 94 CYS SER ILE VAL ARG ILE ASN ARG ASN ARG CYS GLN GLN SEQRES 6 A 94 CYS ARG PHE LYS LYS CYS LEU SER VAL GLY MET SER ARG SEQRES 7 A 94 ASP ALA VAL ARG PHE GLY ARG ILE PRO LYS ARG GLU LYS SEQRES 8 A 94 GLN ARG MET SEQRES 1 B 94 THR LYS LEU ASN GLY MET VAL LEU LEU CYS LYS VAL CYS SEQRES 2 B 94 GLY ASP VAL ALA SER GLY PHE HIS TYR GLY VAL LEU ALA SEQRES 3 B 94 CYS GLU GLY CYS LYS GLY PHE PHE ARG ARG SER ILE GLN SEQRES 4 B 94 GLN ASN ILE GLN TYR LYS ARG CYS LEU LYS ASN GLU ASN SEQRES 5 B 94 CYS SER ILE VAL ARG ILE ASN ARG ASN ARG CYS GLN GLN SEQRES 6 B 94 CYS ARG PHE LYS LYS CYS LEU SER VAL GLY MET SER ARG SEQRES 7 B 94 ASP ALA VAL ARG PHE GLY ARG ILE PRO LYS ARG GLU LYS SEQRES 8 B 94 GLN ARG MET SEQRES 1 E 94 THR LYS LEU ASN GLY MET VAL LEU LEU CYS LYS VAL CYS SEQRES 2 E 94 GLY ASP VAL ALA SER GLY PHE HIS TYR GLY VAL LEU ALA SEQRES 3 E 94 CYS GLU GLY CYS LYS GLY PHE PHE ARG ARG SER ILE GLN SEQRES 4 E 94 GLN ASN ILE GLN TYR LYS ARG CYS LEU LYS ASN GLU ASN SEQRES 5 E 94 CYS SER ILE VAL ARG ILE ASN ARG ASN ARG CYS GLN GLN SEQRES 6 E 94 CYS ARG PHE LYS LYS CYS LEU SER VAL GLY MET SER ARG SEQRES 7 E 94 ASP ALA VAL ARG PHE GLY ARG ILE PRO LYS ARG GLU LYS SEQRES 8 E 94 GLN ARG MET SEQRES 1 F 94 THR LYS LEU ASN GLY MET VAL LEU LEU CYS LYS VAL CYS SEQRES 2 F 94 GLY ASP VAL ALA SER GLY PHE HIS TYR GLY VAL LEU ALA SEQRES 3 F 94 CYS GLU GLY CYS LYS GLY PHE PHE ARG ARG SER ILE GLN SEQRES 4 F 94 GLN ASN ILE GLN TYR LYS ARG CYS LEU LYS ASN GLU ASN SEQRES 5 F 94 CYS SER ILE VAL ARG ILE ASN ARG ASN ARG CYS GLN GLN SEQRES 6 F 94 CYS ARG PHE LYS LYS CYS LEU SER VAL GLY MET SER ARG SEQRES 7 F 94 ASP ALA VAL ARG PHE GLY ARG ILE PRO LYS ARG GLU LYS SEQRES 8 F 94 GLN ARG MET MODRES 1GA5 5IU D 639 DU 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE MODRES 1GA5 5IU H 639 DU 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE HET 5IU D 639 20 HET 5IU H 639 20 HET ZN A 450 1 HET ZN A 451 1 HET ZN B 550 1 HET ZN B 551 1 HET ZN E 450 1 HET ZN E 451 1 HET ZN F 550 1 HET ZN F 551 1 HETNAM 5IU 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION FORMUL 2 5IU 2(C9 H12 I N2 O8 P) FORMUL 9 ZN 8(ZN 2+) FORMUL 17 HOH *279(H2 O) HELIX 1 1 CYS A 18 ILE A 29 1 12 HELIX 2 2 ASN A 49 ARG A 52 5 4 HELIX 3 3 CYS A 53 GLY A 65 1 13 HELIX 4 4 SER A 67 VAL A 71 5 5 HELIX 5 5 CYS B 18 GLN B 30 1 13 HELIX 6 6 CYS B 53 VAL B 64 1 12 HELIX 7 7 SER B 67 VAL B 71 5 5 HELIX 8 8 CYS E 18 GLN E 30 1 13 HELIX 9 9 CYS E 53 VAL E 64 1 12 HELIX 10 10 SER E 67 VAL E 71 5 5 HELIX 11 11 CYS F 18 GLN F 31 1 14 HELIX 12 12 VAL F 46 ARG F 50 5 5 HELIX 13 13 CYS F 53 VAL F 64 1 12 HELIX 14 14 SER F 67 VAL F 71 5 5 SHEET 1 A 2 GLY A 10 HIS A 12 0 SHEET 2 A 2 VAL A 15 ALA A 17 -1 O VAL A 15 N HIS A 12 SHEET 1 B 2 GLY B 10 PHE B 11 0 SHEET 2 B 2 LEU B 16 ALA B 17 -1 N ALA B 17 O GLY B 10 SHEET 1 C 2 GLY E 10 HIS E 12 0 SHEET 2 C 2 VAL E 15 ALA E 17 -1 O VAL E 15 N HIS E 12 SHEET 1 D 2 GLY F 10 PHE F 11 0 SHEET 2 D 2 LEU F 16 ALA F 17 -1 N ALA F 17 O GLY F 10 LINK O3' DT D 638 P 5IU D 639 1555 1555 1.61 LINK O3' 5IU D 639 P DG D 640 1555 1555 3.07 LINK O3' DT H 638 P 5IU H 639 1555 1555 1.61 LINK O3' 5IU H 639 P DG H 640 1555 1555 3.43 LINK SG CYS A 1 ZN ZN A 450 1555 1555 2.11 LINK SG CYS A 4 ZN ZN A 450 1555 1555 2.52 LINK SG CYS A 18 ZN ZN A 450 1555 1555 2.15 LINK SG CYS A 21 ZN ZN A 450 1555 1555 2.36 LINK SG CYS A 37 ZN ZN A 451 1555 1555 2.80 LINK SG CYS A 43 ZN ZN A 451 1555 1555 2.43 LINK SG CYS A 53 ZN ZN A 451 1555 1555 2.44 LINK SG CYS A 56 ZN ZN A 451 1555 1555 2.12 LINK SG CYS B 1 ZN ZN B 550 1555 1555 2.45 LINK SG CYS B 4 ZN ZN B 550 1555 1555 2.27 LINK SG CYS B 18 ZN ZN B 550 1555 1555 1.95 LINK SG CYS B 21 ZN ZN B 550 1555 1555 2.39 LINK SG CYS B 37 ZN ZN B 551 1555 1555 2.30 LINK SG CYS B 43 ZN ZN B 551 1555 1555 1.84 LINK SG CYS B 53 ZN ZN B 551 1555 1555 2.26 LINK SG CYS B 56 ZN ZN B 551 1555 1555 2.56 LINK SG CYS E 1 ZN ZN E 450 1555 1555 2.40 LINK SG CYS E 4 ZN ZN E 450 1555 1555 2.37 LINK SG CYS E 18 ZN ZN E 450 1555 1555 2.02 LINK SG CYS E 21 ZN ZN E 450 1555 1555 2.41 LINK SG CYS E 37 ZN ZN E 451 1555 1555 2.55 LINK SG CYS E 43 ZN ZN E 451 1555 1555 2.96 LINK SG CYS E 53 ZN ZN E 451 1555 1555 2.10 LINK SG CYS E 56 ZN ZN E 451 1555 1555 2.00 LINK SG CYS F 1 ZN ZN F 550 1555 1555 2.25 LINK SG CYS F 4 ZN ZN F 550 1555 1555 2.12 LINK SG CYS F 18 ZN ZN F 550 1555 1555 2.39 LINK SG CYS F 21 ZN ZN F 550 1555 1555 2.10 LINK SG CYS F 37 ZN ZN F 551 1555 1555 2.30 LINK SG CYS F 43 ZN ZN F 551 1555 1555 2.15 LINK SG CYS F 53 ZN ZN F 551 1555 1555 2.48 LINK SG CYS F 56 ZN ZN F 551 1555 1555 2.37 SITE 1 AC1 4 CYS A 1 CYS A 4 CYS A 18 CYS A 21 SITE 1 AC2 4 CYS A 37 CYS A 43 CYS A 53 CYS A 56 SITE 1 AC3 4 CYS B 1 CYS B 4 CYS B 18 CYS B 21 SITE 1 AC4 4 CYS B 37 CYS B 43 CYS B 53 CYS B 56 SITE 1 AC5 4 CYS E 1 CYS E 4 CYS E 18 CYS E 21 SITE 1 AC6 4 CYS E 37 CYS E 43 CYS E 53 CYS E 56 SITE 1 AC7 4 CYS F 1 CYS F 4 CYS F 18 CYS F 21 SITE 1 AC8 4 CYS F 37 CYS F 43 CYS F 53 CYS F 56 CRYST1 44.920 52.020 78.880 85.84 76.61 74.48 P 1 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 0.022262 -0.006182 -0.005230 0.00000 SCALE2 0.000000 0.019951 -0.000225 0.00000 SCALE3 0.000000 0.000000 0.013033 0.00000 CONECT 762 791 CONECT 774 775 779 783 CONECT 775 774 776 780 CONECT 776 775 777 CONECT 777 776 778 781 CONECT 778 777 779 782 CONECT 779 774 778 CONECT 780 775 CONECT 781 777 CONECT 782 778 CONECT 783 774 784 788 CONECT 784 783 785 CONECT 785 784 786 787 CONECT 786 785 788 789 CONECT 787 785 794 CONECT 788 783 786 CONECT 789 786 790 CONECT 790 789 791 CONECT 791 762 790 792 793 CONECT 792 791 CONECT 793 791 CONECT 794 787 CONECT 1578 1607 CONECT 1590 1591 1595 1599 CONECT 1591 1590 1592 1596 CONECT 1592 1591 1593 CONECT 1593 1592 1594 1597 CONECT 1594 1593 1595 1598 CONECT 1595 1590 1594 CONECT 1596 1591 CONECT 1597 1593 CONECT 1598 1594 CONECT 1599 1590 1600 1604 CONECT 1600 1599 1601 CONECT 1601 1600 1602 1603 CONECT 1602 1601 1604 1605 CONECT 1603 1601 1610 CONECT 1604 1599 1602 CONECT 1605 1602 1606 CONECT 1606 1605 1607 CONECT 1607 1578 1606 1608 1609 CONECT 1608 1607 CONECT 1609 1607 CONECT 1610 1603 CONECT 1661 4000 CONECT 1679 4000 CONECT 1776 4000 CONECT 1795 4000 CONECT 1923 4001 CONECT 1964 4001 CONECT 2042 4001 CONECT 2062 4001 CONECT 2263 4002 CONECT 2285 4002 CONECT 2382 4002 CONECT 2401 4002 CONECT 2532 4003 CONECT 2570 4003 CONECT 2648 4003 CONECT 2668 4003 CONECT 2851 4004 CONECT 2873 4004 CONECT 2970 4004 CONECT 2989 4004 CONECT 3128 4005 CONECT 3162 4005 CONECT 3240 4005 CONECT 3264 4005 CONECT 3453 4006 CONECT 3475 4006 CONECT 3572 4006 CONECT 3591 4006 CONECT 3715 4007 CONECT 3760 4007 CONECT 3844 4007 CONECT 3868 4007 CONECT 4000 1661 1679 1776 1795 CONECT 4001 1923 1964 2042 2062 CONECT 4002 2263 2285 2382 2401 CONECT 4003 2532 2570 2648 2668 CONECT 4004 2851 2873 2970 2989 CONECT 4005 3128 3162 3240 3264 CONECT 4006 3453 3475 3572 3591 CONECT 4007 3715 3760 3844 3868 MASTER 510 0 10 14 8 0 8 6 4278 8 84 40 END