HEADER TRANSCRIPTION 03-APR-08 3CQV TITLE CRYSTAL STRUCTURE OF REVERB BETA IN COMPLEX WITH HEME COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEAR RECEPTOR SUBFAMILY 1 GROUP D MEMBER 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 381-579, SEE REMARKS 200 AND 999; COMPND 5 SYNONYM: REV-ERB-BETA, EAR-1R, ORPHAN NUCLEAR HORMONE RECEPTOR BD73; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 GENE: NR1D2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 PLYSE; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS REVERB BETA, HEME, NR1D2, NUCLEAR RECEPTOR, DNA-BINDING, METAL- KEYWDS 2 BINDING, NUCLEUS, REPRESSOR, TRANSCRIPTION, TRANSCRIPTION KEYWDS 3 REGULATION, ZINC, ZINC-FINGER, STRUCTURAL GENOMICS, STRUCTURAL KEYWDS 4 GENOMICS CONSORTIUM, SGC EXPDTA X-RAY DIFFRACTION AUTHOR X.XU,A.DONG,K.I.PARDEE,J.REINKING,H.KRAUSE,A.SCHUETZ,R.ZHANG,H.CUI, AUTHOR 2 A.EDWARDS,C.H.ARROWSMITH,J.WEIGELT,C.BOUNTRA,A.SAVCHENKO, AUTHOR 3 A.BOTCHKAREV,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 4 13-NOV-24 3CQV 1 REMARK LINK REVDAT 3 28-APR-09 3CQV 1 JRNL REVDAT 2 24-FEB-09 3CQV 1 VERSN REVDAT 1 05-AUG-08 3CQV 0 JRNL AUTH K.I.PARDEE,X.XU,J.REINKING,A.SCHUETZ,A.DONG,S.LIU,R.ZHANG, JRNL AUTH 2 J.TIEFENBACH,G.LAJOIE,A.N.PLOTNIKOV,A.BOTCHKAREV,H.M.KRAUSE, JRNL AUTH 3 A.EDWARDS JRNL TITL THE STRUCTURAL BASIS OF GAS-RESPONSIVE TRANSCRIPTION BY THE JRNL TITL 2 HUMAN NUCLEAR HORMONE RECEPTOR REV-ERBBETA. JRNL REF PLOS BIOL. V. 7 E43 2009 JRNL REFN ISSN 1544-9173 JRNL PMID 19243223 JRNL DOI 10.1371/JOURNAL.PBIO.1000043 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 19007 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1020 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1391 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.2050 REMARK 3 BIN FREE R VALUE SET COUNT : 72 REMARK 3 BIN FREE R VALUE : 0.2590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1540 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 157 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.15000 REMARK 3 B22 (A**2) : -0.30000 REMARK 3 B33 (A**2) : 0.16000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.147 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.139 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.083 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.679 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1654 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2254 ; 1.426 ; 2.047 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 203 ; 4.730 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 70 ;31.759 ;24.429 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 290 ;13.663 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;11.069 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 250 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1239 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 838 ; 0.208 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1162 ; 0.305 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 111 ; 0.173 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 37 ; 0.220 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.253 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1027 ; 1.596 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1625 ; 1.840 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 695 ; 3.337 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 627 ; 5.029 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. PROGRAM COOT 0.3.3 HAS ALSO BEEN USED IN REFINEMENT REMARK 4 REMARK 4 3CQV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-APR-08. REMARK 100 THE DEPOSITION ID IS D_1000047103. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20061 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : 0.09000 REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.40 REMARK 200 R MERGE FOR SHELL (I) : 0.45300 REMARK 200 R SYM FOR SHELL (I) : 0.45300 REMARK 200 FOR SHELL : 5.460 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE CRYSTAL WAS OBTAINED BY IN SITU PROTEOLYSIS. PROTEIN REMARK 200 SAMPLE WAS MIXED WITH 1:2000 (W/W, PROTEASE TO PROTEIN) RATIO REMARK 200 WITH TRYPSIN DURING CONCENTRATION. THE MATTHEWS COEFFICIENT REMARK 200 CALCULATED BASED ON THE CONSTRUCTED SEQUENCE IS 1.94, AND REMARK 200 SOLVENT CONTENT 36.7%. THE VALUES SHOWN IN FILE ARE CALCULATED REMARK 200 BASED ON THE SEQUENCE STARTING FROM THE FIRST VISIBLE N-TERMINAL REMARK 200 RESIDUE IN ELECTRON DENSITY, THEREFORE THEY MAY NOT BE ACCURATE. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M AMMONIUM SULFATE, 0.1 M NA HEPES REMARK 280 PH 7.6, 4% JEFFAMINE M-600, VAPOR DIFFUSION, TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 36.71400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.31150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.71400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.31150 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 HOH A 730 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 VAL A 577 REMARK 465 HIS A 578 REMARK 465 PRO A 579 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 388 CD CE NZ REMARK 470 GLU A 404 CD OE1 OE2 REMARK 470 LYS A 439 CE NZ REMARK 470 LYS A 467 CE NZ REMARK 470 LYS A 576 CG CD CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASN A 566 ND2 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 OE1 GLU A 415 NH1 ARG A 449 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 824 O HOH A 824 2755 1.99 REMARK 500 REMARK 500 REMARK: NULL 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 ASN A 566 CG ASN A 566 ND2 -0.169 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 GLN A 497 68.21 33.06 REMARK 500 ASP A 515 127.18 -39.67 REMARK 500 GLU A 547 57.21 -143.13 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 ASN A 566 0.07 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 HEM A 601 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 384 SG REMARK 620 2 HEM A 601 NA 94.7 REMARK 620 3 HEM A 601 NB 87.2 90.8 REMARK 620 4 HEM A 601 NC 86.0 178.1 87.5 REMARK 620 5 HEM A 601 ND 94.1 88.2 178.5 93.5 REMARK 620 6 HIS A 568 NE2 172.5 88.6 86.0 90.5 92.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 601 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE COMPLETE SEQUENCE OF THE CONSTRUCT USED FOR REMARK 999 CRYSTALLIZATION IS: REMARK 999 MHHHHHHSSGRENLYFQGSSPPSSDFAKEEVIGMVTRAHKDTFMYNQEQQENVPIDGFS REMARK 999 QNENKNSYLCNTGGRMHLVCPMSKSPYVDPHKSGHEIWEEFSMSFTPAVKEVVEFAKRI REMARK 999 PGFRDLSQHDQVNLLKAGTFEVLMVRFASLFDAKERTVTFLSGKKYSVDDLHSMGAGDL REMARK 999 LNSMFEFSEKLNALQLSDEEMSLFTAVVLVSADRSGIENVNSVEALQETLIRALRTLIM REMARK 999 KNHPNEASIFTKLLLKLPDLRSLNNMHSEELLAFKVHP, FROM WHICH REMARK 999 MHHHHHHSSGRENLYFQG IS AN N-TERMINAL EXPRESSION TAG FOLLOWED REMARK 999 BY THE SEQUENCE OF A FUSION PROTEIN, CONTAINING RESIDUES REMARK 999 241-274 OF UNIPROT ENTRY Q14995 (NR1D2_HUMAN): REMARK 999 SSPPSSDFAKEEVIGMVTRAHKDTFMYNQEQQEN, AND RESIDUES 358-579 OF REMARK 999 UNIPROT ENTRY Q14995 (NR1D2_HUMAN): REMARK 999 VPIDGFSQNENKNSYLCNTGGRMHLVCPMSKSPYVDPHKSGHEIWEEFSMSFTPAVKEV REMARK 999 VEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFDAKERTVTFLSGKKYSVDDLH REMARK 999 SMGAGDLLNSMFEFSEKLNALQLSDEEMSLFTAVVLVSADRSGIENVNSVEALQETLIR REMARK 999 ALRTLIMKNHPNEASIFTKLLLKLPDLRSLNNMHSEELLAFKVHP. REMARK 999 AUTHORS STATE THAT THE PROTEIN SAMPLE WAS MIXED WITH 1:2000 REMARK 999 (W/W, PROTEASE TO PROTEIN) RATIO WITH TRYPSIN DURING REMARK 999 CONCENTRATION, WHICH EVIDENTLY CLEAVED OFF MANY OF REMARK 999 N-TERMINAL RESIDUES OF THE PROTEIN PRIOR TO CRYSTAL REMARK 999 FORMATION. THE PRECISE LOCATION OF THE CLEAVAGE SITE HAS NOT REMARK 999 BEEN DETERMINED. REMARK 999 THEREFORE, THE SEQUENCE INFORMATION, AS WELL AS THE VALUES REMARK 999 OF MATTHEWS COEFFICIENT AND SOLVENT CONTENT ARE BASED ON REMARK 999 THE CHAIN LENGTH STARTING FROM THE FIRST VISIBLE N-TERMINAL REMARK 999 RESIDUE IN ELECTRON DENSITY. DBREF 3CQV A 381 579 UNP Q14995 NR1D2_HUMAN 381 579 SEQRES 1 A 199 HIS LEU VAL CYS PRO MSE SER LYS SER PRO TYR VAL ASP SEQRES 2 A 199 PRO HIS LYS SER GLY HIS GLU ILE TRP GLU GLU PHE SER SEQRES 3 A 199 MSE SER PHE THR PRO ALA VAL LYS GLU VAL VAL GLU PHE SEQRES 4 A 199 ALA LYS ARG ILE PRO GLY PHE ARG ASP LEU SER GLN HIS SEQRES 5 A 199 ASP GLN VAL ASN LEU LEU LYS ALA GLY THR PHE GLU VAL SEQRES 6 A 199 LEU MSE VAL ARG PHE ALA SER LEU PHE ASP ALA LYS GLU SEQRES 7 A 199 ARG THR VAL THR PHE LEU SER GLY LYS LYS TYR SER VAL SEQRES 8 A 199 ASP ASP LEU HIS SER MSE GLY ALA GLY ASP LEU LEU ASN SEQRES 9 A 199 SER MSE PHE GLU PHE SER GLU LYS LEU ASN ALA LEU GLN SEQRES 10 A 199 LEU SER ASP GLU GLU MSE SER LEU PHE THR ALA VAL VAL SEQRES 11 A 199 LEU VAL SER ALA ASP ARG SER GLY ILE GLU ASN VAL ASN SEQRES 12 A 199 SER VAL GLU ALA LEU GLN GLU THR LEU ILE ARG ALA LEU SEQRES 13 A 199 ARG THR LEU ILE MSE LYS ASN HIS PRO ASN GLU ALA SER SEQRES 14 A 199 ILE PHE THR LYS LEU LEU LEU LYS LEU PRO ASP LEU ARG SEQRES 15 A 199 SER LEU ASN ASN MSE HIS SER GLU GLU LEU LEU ALA PHE SEQRES 16 A 199 LYS VAL HIS PRO MODRES 3CQV MSE A 386 MET SELENOMETHIONINE MODRES 3CQV MSE A 407 MET SELENOMETHIONINE MODRES 3CQV MSE A 447 MET SELENOMETHIONINE MODRES 3CQV MSE A 477 MET SELENOMETHIONINE MODRES 3CQV MSE A 486 MET SELENOMETHIONINE MODRES 3CQV MSE A 503 MET SELENOMETHIONINE MODRES 3CQV MSE A 541 MET SELENOMETHIONINE MODRES 3CQV MSE A 567 MET SELENOMETHIONINE HET MSE A 386 8 HET MSE A 407 8 HET MSE A 447 8 HET MSE A 477 8 HET MSE A 486 8 HET MSE A 503 8 HET MSE A 541 8 HET MSE A 567 8 HET HEM A 601 43 HETNAM MSE SELENOMETHIONINE HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 HOH *157(H2 O) HELIX 1 1 SER A 397 ARG A 422 1 26 HELIX 2 2 ILE A 423 LEU A 429 5 7 HELIX 3 3 SER A 430 PHE A 450 1 21 HELIX 4 4 VAL A 471 MSE A 477 1 7 HELIX 5 5 GLY A 480 ALA A 495 1 16 HELIX 6 6 SER A 499 SER A 513 1 15 HELIX 7 7 ASN A 521 HIS A 544 1 24 HELIX 8 8 ALA A 548 ALA A 574 1 27 SHEET 1 A 3 PHE A 454 ASP A 455 0 SHEET 2 A 3 THR A 460 THR A 462 -1 O THR A 460 N ASP A 455 SHEET 3 A 3 LYS A 468 SER A 470 -1 O TYR A 469 N VAL A 461 LINK C PRO A 385 N MSE A 386 1555 1555 1.33 LINK C MSE A 386 N SER A 387 1555 1555 1.34 LINK C SER A 406 N MSE A 407 1555 1555 1.32 LINK C MSE A 407 N SER A 408 1555 1555 1.34 LINK C LEU A 446 N MSE A 447 1555 1555 1.33 LINK C MSE A 447 N VAL A 448 1555 1555 1.34 LINK C SER A 476 N MSE A 477 1555 1555 1.33 LINK C MSE A 477 N GLY A 478 1555 1555 1.33 LINK C SER A 485 N MSE A 486 1555 1555 1.33 LINK C MSE A 486 N PHE A 487 1555 1555 1.34 LINK C GLU A 502 N MSE A 503 1555 1555 1.33 LINK C MSE A 503 N SER A 504 1555 1555 1.33 LINK C ILE A 540 N MSE A 541 1555 1555 1.33 LINK C MSE A 541 N ALYS A 542 1555 1555 1.33 LINK C MSE A 541 N BLYS A 542 1555 1555 1.32 LINK C AASN A 566 N MSE A 567 1555 1555 1.33 LINK C BASN A 566 N MSE A 567 1555 1555 1.33 LINK C MSE A 567 N HIS A 568 1555 1555 1.32 LINK SG CYS A 384 FE HEM A 601 1555 1555 2.34 LINK NE2 HIS A 568 FE HEM A 601 1555 1555 2.16 SITE 1 AC1 20 HIS A 381 LEU A 382 CYS A 384 PRO A 385 SITE 2 AC1 20 PHE A 405 PHE A 409 PHE A 443 LEU A 446 SITE 3 AC1 20 PHE A 454 ALA A 479 GLY A 480 LEU A 482 SITE 4 AC1 20 LEU A 483 HIS A 568 GLU A 571 PHE A 575 SITE 5 AC1 20 HOH A 767 HOH A 802 HOH A 857 HOH A 900 CRYST1 73.428 48.623 68.954 90.00 90.00 90.00 P 21 21 2 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 0.013619 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020566 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014502 0.00000