HEADER CIRCADIAN CLOCK PROTEIN 05-DEC-15 5F69 TITLE DROSOPHILA MELANOGASTER CYCLE W398A PAS-B WITH BOUND GLYCEROL 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, GLYCEROL, CLOCK, BMAL, CIRCADIAN CLOCK PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.C.MANAHAN,B.R.CRANE REVDAT 2 06-MAR-24 5F69 1 REMARK REVDAT 1 07-DEC-16 5F69 0 JRNL AUTH C.C.MANAHAN,B.R.CRANE JRNL TITL DROSOPHILA MELANOGASTER CYCLE PAS-B WITH BOUND GLYCEROL JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.37 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) : 1.37 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 23104 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.650 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 22.2019 - 3.3069 1.00 1578 149 0.1571 0.1768 REMARK 3 2 3.3069 - 2.6262 1.00 1551 148 0.1672 0.1789 REMARK 3 3 2.6262 - 2.2946 1.00 1534 145 0.1626 0.2071 REMARK 3 4 2.2946 - 2.0850 1.00 1559 147 0.1507 0.1875 REMARK 3 5 2.0850 - 1.9356 1.00 1497 142 0.1559 0.1707 REMARK 3 6 1.9356 - 1.8216 1.00 1555 148 0.1617 0.1989 REMARK 3 7 1.8216 - 1.7304 1.00 1526 144 0.1694 0.2160 REMARK 3 8 1.7304 - 1.6551 1.00 1518 144 0.1764 0.2256 REMARK 3 9 1.6551 - 1.5914 1.00 1520 144 0.1806 0.2036 REMARK 3 10 1.5914 - 1.5365 1.00 1523 144 0.1947 0.2108 REMARK 3 11 1.5365 - 1.4884 1.00 1520 143 0.2164 0.2546 REMARK 3 12 1.4884 - 1.4459 1.00 1544 147 0.2371 0.2899 REMARK 3 13 1.4459 - 1.4078 0.96 1455 137 0.2678 0.2996 REMARK 3 14 1.4078 - 1.3735 0.80 1225 117 0.2860 0.3307 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.07 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.93 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 : 0.013 878 REMARK 3 ANGLE : 1.263 1181 REMARK 3 CHIRALITY : 0.121 125 REMARK 3 PLANARITY : 0.010 150 REMARK 3 DIHEDRAL : 18.073 323 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): 153.7908 4.0017 16.8707 REMARK 3 T TENSOR REMARK 3 T11: 0.1299 T22: 0.1309 REMARK 3 T33: 0.1481 T12: 0.0047 REMARK 3 T13: -0.0023 T23: -0.0016 REMARK 3 L TENSOR REMARK 3 L11: 0.9643 L22: 0.9582 REMARK 3 L33: 0.5574 L12: 0.5846 REMARK 3 L13: -0.0544 L23: -0.2426 REMARK 3 S TENSOR REMARK 3 S11: 0.0147 S12: 0.0143 S13: 0.0007 REMARK 3 S21: -0.0022 S22: 0.0167 S23: -0.0164 REMARK 3 S31: -0.0121 S32: 0.0028 S33: -0.0318 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 5F69 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_1000216095. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-15 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) : 0.987 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 : 23120 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.370 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 (%) : 98.3 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.53800 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 (%): 47.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 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 36.64900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.19900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 36.64900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.19900 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: 260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 1.84 REMARK 500 O HOH A 672 O HOH A 715 1.98 REMARK 500 N MET A 310 O ASN A 409 2.01 REMARK 500 NZ LYS A 369 CB GLU A 390 2.05 REMARK 500 O HOH A 629 O HOH A 695 2.13 REMARK 500 O HOH A 664 O HOH A 698 2.13 REMARK 500 O HOH A 668 O HOH A 703 2.13 REMARK 500 O HOH A 643 O HOH A 662 2.18 REMARK 500 O HOH A 631 O HOH A 664 2.18 REMARK 500 O HOH A 692 O HOH A 736 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 PHE A 344 CB - CG - CD1 ANGL. DEV. = 4.5 DEGREES 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 42.34 -92.21 REMARK 500 SER A 400 -0.79 73.31 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 GOL A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5F68 RELATED DB: PDB REMARK 900 RELATED ID: 5F5Y RELATED DB: PDB REMARK 900 RELATED ID: 5F6A RELATED DB: PDB DBREF 5F69 A 311 412 UNP O61734 CYCL_DROME 311 412 SEQADV 5F69 MET A 310 UNP O61734 INITIATING METHIONINE SEQADV 5F69 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 GOL A 501 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *142(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 PHE A 412 -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 PHE A 412 -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 10 PHE A 311 SER A 313 HIS A 315 PHE A 321 SITE 2 AC1 10 PHE A 348 TYR A 375 PHE A 377 SER A 389 SITE 3 AC1 10 TRP A 391 ASN A 409 CRYST1 73.298 44.398 38.502 90.00 114.75 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 0.013643 0.000000 0.006288 0.00000 SCALE2 0.000000 0.022524 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028599 0.00000