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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
