HEADER CIRCADIAN CLOCK PROTEIN 14-FEB-19 6QPJ TITLE HUMAN CLOCK PAS-A DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CIRCADIAN LOCOMOTER OUTPUT CYCLES PROTEIN KAPUT; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HCLOCK,CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 8,BHLHE8; COMPND 5 EC: 2.3.1.48; COMPND 6 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: CLOCK, BHLHE8, KIAA0334; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CIRCADIAN, CLOCK, PAS, CIRCADIAN CLOCK PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.KWON,S.L.FREEMAN,P.C.E.MOODY,E.L.RAVEN,J.BASRAN REVDAT 4 15-MAY-24 6QPJ 1 REMARK REVDAT 3 09-OCT-19 6QPJ 1 JRNL REVDAT 2 02-OCT-19 6QPJ 1 JRNL REVDAT 1 25-SEP-19 6QPJ 0 JRNL AUTH S.L.FREEMAN,H.KWON,N.PORTOLANO,G.PARKIN, JRNL AUTH 2 U.VENKATRAMAN GIRIJA,J.BASRAN,A.J.FIELDING,L.FAIRALL, JRNL AUTH 3 D.A.SVISTUNENKO,P.C.E.MOODY,J.W.R.SCHWABE,C.P.KYRIACOU, JRNL AUTH 4 E.L.RAVEN JRNL TITL HEME BINDING TO HUMAN CLOCK AFFECTS INTERACTIONS WITH THE JRNL TITL 2 E-BOX. JRNL REF PROC.NATL.ACAD.SCI.USA V. 116 19911 2019 JRNL REFN ESSN 1091-6490 JRNL PMID 31527239 JRNL DOI 10.1073/PNAS.1905216116 REMARK 2 REMARK 2 RESOLUTION. 2.32 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 6783 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.360 REMARK 3 FREE R VALUE TEST SET COUNT : 296 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 25.0644 - 2.9160 1.00 3333 156 0.1822 0.2129 REMARK 3 2 2.9160 - 2.3150 0.97 3154 140 0.1731 0.3240 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 1083 REMARK 3 ANGLE : 1.001 1466 REMARK 3 CHIRALITY : 0.054 170 REMARK 3 PLANARITY : 0.006 186 REMARK 3 DIHEDRAL : 3.345 653 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6QPJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1292100613. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-AUG-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6784 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM MES PH 6.5 0.1M MAGNESIUM REMARK 280 SULFATE 20 % PEG 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-Z+1/2 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 20.71144 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.68000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.76853 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 20.71144 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.68000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 37.76853 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 344 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 SER A 224 REMARK 465 VAL A 225 REMARK 465 SER A 226 REMARK 465 SER A 227 REMARK 465 SER A 228 REMARK 465 ALA A 229 REMARK 465 HIS A 230 REMARK 465 ASN A 231 REMARK 465 GLY A 232 REMARK 465 PHE A 233 REMARK 465 GLU A 234 REMARK 465 GLY A 235 REMARK 465 THR A 236 REMARK 465 ILE A 237 REMARK 465 GLN A 238 REMARK 465 ARG A 239 REMARK 465 THR A 240 REMARK 465 HIS A 241 REMARK 465 ARG A 242 REMARK 465 PRO A 243 REMARK 465 SER A 244 REMARK 465 TYR A 245 REMARK 465 GLU A 246 REMARK 465 GLN A 261 REMARK 465 PHE A 262 REMARK 465 ILE A 263 REMARK 465 LYS A 264 REMARK 465 GLU A 265 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 OD1 ASP A 151 O HOH A 301 2.14 REMARK 500 O HOH A 365 O HOH A 366 2.15 REMARK 500 OG SER A 137 O HOH A 302 2.18 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 TYR A 184 55.57 -119.90 REMARK 500 LEU A 185 -91.08 -105.87 REMARK 500 LYS A 186 108.11 63.51 REMARK 500 CYS A 195 174.79 179.53 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 A 372 DISTANCE = 6.79 ANGSTROMS DBREF 6QPJ A 106 265 UNP O15516 CLOCK_HUMAN 106 265 SEQADV 6QPJ MET A 105 UNP O15516 INITIATING METHIONINE SEQRES 1 A 161 MET SER ASN GLU GLU PHE THR GLN LEU MET LEU GLU ALA SEQRES 2 A 161 LEU ASP GLY PHE PHE LEU ALA ILE MET THR ASP GLY SER SEQRES 3 A 161 ILE ILE TYR VAL SER GLU SER VAL THR SER LEU LEU GLU SEQRES 4 A 161 HIS LEU PRO SER ASP LEU VAL ASP GLN SER ILE PHE ASN SEQRES 5 A 161 PHE ILE PRO GLU GLY GLU HIS SER GLU VAL TYR LYS ILE SEQRES 6 A 161 LEU SER THR HIS LEU LEU GLU SER ASP SER LEU THR PRO SEQRES 7 A 161 GLU TYR LEU LYS SER LYS ASN GLN LEU GLU PHE CYS CYS SEQRES 8 A 161 HIS MET LEU ARG GLY THR ILE ASP PRO LYS GLU PRO SER SEQRES 9 A 161 THR TYR GLU TYR VAL LYS PHE ILE GLY ASN PHE LYS SER SEQRES 10 A 161 LEU ASN SER VAL SER SER SER ALA HIS ASN GLY PHE GLU SEQRES 11 A 161 GLY THR ILE GLN ARG THR HIS ARG PRO SER TYR GLU ASP SEQRES 12 A 161 ARG VAL CYS PHE VAL ALA THR VAL ARG LEU ALA THR PRO SEQRES 13 A 161 GLN PHE ILE LYS GLU FORMUL 2 HOH *72(H2 O) HELIX 1 AA1 SER A 106 ASP A 119 1 14 HELIX 2 AA2 SER A 137 GLU A 143 1 7 HELIX 3 AA3 LEU A 145 VAL A 150 1 6 HELIX 4 AA4 SER A 153 PHE A 157 5 5 HELIX 5 AA5 PRO A 159 GLY A 161 5 3 HELIX 6 AA6 GLU A 162 LEU A 175 1 14 HELIX 7 AA7 THR A 181 LEU A 185 5 5 SHEET 1 AA1 5 ILE A 131 VAL A 134 0 SHEET 2 AA1 5 GLY A 120 MET A 126 -1 N ALA A 124 O ILE A 132 SHEET 3 AA1 5 VAL A 249 LEU A 257 -1 O VAL A 255 N PHE A 121 SHEET 4 AA1 5 TYR A 210 SER A 221 -1 N LYS A 214 O ARG A 256 SHEET 5 AA1 5 LEU A 191 LEU A 198 -1 N PHE A 193 O PHE A 215 CRYST1 45.990 45.360 75.675 90.00 93.46 90.00 I 1 2 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 0.021744 0.000000 0.001314 0.00000 SCALE2 0.000000 0.022046 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013239 0.00000