HEADER CIRCADIAN CLOCK PROTEIN 05-DEC-15 5F68 TITLE DROSOPHILA MELANOGASTER CYCLE W398A PAS-B WITH BOUND ETHYLENE GLYCOL COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN CYCLE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BRAIN AND MUSCLE ARNT-LIKE 1,BMAL1,MOP3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: CYC, CG8727; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PAS, ETHYLENE GLYCOL, CLOCK, BMAL, CIRCADIAN CLOCK PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.C.MANAHAN,B.R.CRANE REVDAT 2 06-MAR-24 5F68 1 REMARK REVDAT 1 07-DEC-16 5F68 0 JRNL AUTH C.C.MANAHAN,B.R.CRANE JRNL TITL DROSOPHILA MELANOGASTER CYCLE PAS-B WITH BOUND ETHYLENE JRNL TITL 2 GLYCOL JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 3 NUMBER OF REFLECTIONS : 30172 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.610 REMARK 3 FREE R VALUE TEST SET COUNT : 1994 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 34.9295 - 2.9648 0.98 2179 154 0.1694 0.1836 REMARK 3 2 2.9648 - 2.3534 1.00 2180 154 0.1812 0.1887 REMARK 3 3 2.3534 - 2.0560 1.00 2184 155 0.1582 0.1940 REMARK 3 4 2.0560 - 1.8680 1.00 2163 153 0.1561 0.1760 REMARK 3 5 1.8680 - 1.7341 1.00 2164 153 0.1662 0.1739 REMARK 3 6 1.7341 - 1.6319 1.00 2143 152 0.1577 0.1761 REMARK 3 7 1.6319 - 1.5501 1.00 2171 154 0.1728 0.1948 REMARK 3 8 1.5501 - 1.4827 1.00 2128 150 0.1948 0.2022 REMARK 3 9 1.4827 - 1.4256 0.98 2137 151 0.2115 0.2110 REMARK 3 10 1.4256 - 1.3764 0.95 2048 145 0.2274 0.2228 REMARK 3 11 1.3764 - 1.3334 0.89 1914 137 0.2437 0.2942 REMARK 3 12 1.3334 - 1.2952 0.82 1775 124 0.2426 0.2669 REMARK 3 13 1.2952 - 1.2611 0.74 1599 114 0.2535 0.2675 REMARK 3 14 1.2611 - 1.2304 0.64 1393 98 0.2509 0.2464 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.57 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 : 0.012 883 REMARK 3 ANGLE : 1.266 1189 REMARK 3 CHIRALITY : 0.123 126 REMARK 3 PLANARITY : 0.010 152 REMARK 3 DIHEDRAL : 13.837 325 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 80.4771 17.9789 16.7144 REMARK 3 T TENSOR REMARK 3 T11: 0.0658 T22: 0.0595 REMARK 3 T33: 0.0646 T12: -0.0015 REMARK 3 T13: 0.0036 T23: -0.0029 REMARK 3 L TENSOR REMARK 3 L11: 0.3955 L22: 0.4453 REMARK 3 L33: 0.2463 L12: 0.2587 REMARK 3 L13: 0.0807 L23: -0.0860 REMARK 3 S TENSOR REMARK 3 S11: 0.0111 S12: 0.0064 S13: -0.0081 REMARK 3 S21: -0.0170 S22: 0.0166 S23: -0.0177 REMARK 3 S31: -0.0162 S32: -0.0004 S33: 0.0122 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 5F68 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1000216094. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : .987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30239 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.230 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 63.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.54100 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K 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 36.65400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.08450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 36.65400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.08450 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 3.0 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 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 NZ LYS A 369 OE1 GLU A 390 1.85 REMARK 500 O HOH A 700 O HOH A 706 1.94 REMARK 500 O HOH A 616 O HOH A 631 2.00 REMARK 500 O HOH A 665 O HOH A 674 2.06 REMARK 500 O HOH A 664 O HOH A 700 2.07 REMARK 500 O HOH A 611 O HOH A 686 2.14 REMARK 500 NZ LYS A 369 CD GLU A 390 2.18 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 661 O HOH A 669 4756 2.11 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 PRO A 367 46.42 -94.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5F6A RELATED DB: PDB REMARK 900 RELATED ID: 5F68 RELATED DB: PDB REMARK 900 RELATED ID: 5F5Y RELATED DB: PDB DBREF 5F68 A 311 412 UNP O61734 CYCL_DROME 311 412 SEQADV 5F68 MET A 310 UNP O61734 INITIATING METHIONINE SEQADV 5F68 ALA A 398 UNP O61734 TRP 398 ENGINEERED MUTATION SEQRES 1 A 103 MET PHE ILE SER ARG HIS SER GLY GLU GLY LYS PHE LEU SEQRES 2 A 103 PHE ILE ASP GLN ARG ALA THR LEU VAL ILE GLY PHE LEU SEQRES 3 A 103 PRO GLN GLU ILE LEU GLY THR SER PHE TYR GLU TYR PHE SEQRES 4 A 103 HIS ASN GLU ASP ILE ALA ALA LEU MET GLU SER HIS LYS SEQRES 5 A 103 MET VAL MET GLN VAL PRO GLU LYS VAL THR THR GLN VAL SEQRES 6 A 103 TYR ARG PHE ARG CYS LYS ASP ASN SER TYR ILE GLN LEU SEQRES 7 A 103 GLN SER GLU TRP ARG ALA PHE LYS ASN PRO ALA THR SER SEQRES 8 A 103 GLU ILE ASP TYR ILE ILE ALA LYS ASN SER VAL PHE HET EDO A 501 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO C2 H6 O2 FORMUL 3 HOH *107(H2 O) HELIX 1 AA1 ARG A 327 GLY A 333 1 7 HELIX 2 AA2 LEU A 335 LEU A 340 1 6 HELIX 3 AA3 SER A 343 TYR A 347 5 5 HELIX 4 AA4 ASP A 352 VAL A 366 1 15 SHEET 1 AA1 5 PHE A 321 ILE A 324 0 SHEET 2 AA1 5 PHE A 311 HIS A 315 -1 N ARG A 314 O LEU A 322 SHEET 3 AA1 5 ILE A 402 VAL A 411 -1 O ASN A 409 N PHE A 311 SHEET 4 AA1 5 TYR A 384 LYS A 395 -1 N GLN A 388 O SER A 410 SHEET 5 AA1 5 VAL A 370 THR A 371 -1 N VAL A 370 O TRP A 391 SHEET 1 AA2 5 PHE A 321 ILE A 324 0 SHEET 2 AA2 5 PHE A 311 HIS A 315 -1 N ARG A 314 O LEU A 322 SHEET 3 AA2 5 ILE A 402 VAL A 411 -1 O ASN A 409 N PHE A 311 SHEET 4 AA2 5 TYR A 384 LYS A 395 -1 N GLN A 388 O SER A 410 SHEET 5 AA2 5 TYR A 375 ARG A 378 -1 N PHE A 377 O ILE A 385 SITE 1 AC1 8 HIS A 315 PHE A 348 TYR A 375 PHE A 377 SITE 2 AC1 8 SER A 389 TRP A 391 ALA A 407 ASN A 409 CRYST1 73.308 44.169 38.574 90.00 115.16 90.00 C 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 0.013641 0.000000 0.006406 0.00000 SCALE2 0.000000 0.022640 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028641 0.00000