HEADER RNA 24-AUG-24 9JA7 TITLE CRYSTAL STRUCTURE OF THEOPHYLLINE APTAMER OBTAINED IN THE PRESENCE OF TITLE 2 CAFFEINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THEOPHYLLINE APTAMER; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS THEOPHYLLINE APTAMER, CAFFEINE, RNA EXPDTA X-RAY DIFFRACTION AUTHOR J.KONDO,Y.OHTANI REVDAT 1 03-SEP-25 9JA7 0 JRNL AUTH J.KONDO,Y.OHTANI JRNL TITL CRYSTAL STRUCTURE OF THEOPHYLLINE APTAMER OBTAINED IN THE JRNL TITL 2 PRESENCE OF CAFFEINE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487) 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) : 2.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 6785 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.980 REMARK 3 FREE R VALUE TEST SET COUNT : 677 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 33.6600 - 4.4300 1.00 1241 140 0.1527 0.2080 REMARK 3 2 4.4300 - 3.5200 1.00 1244 130 0.1880 0.2460 REMARK 3 3 3.5200 - 3.0700 0.97 1191 143 0.2529 0.2893 REMARK 3 4 3.0700 - 2.7900 0.98 1215 131 0.3102 0.3578 REMARK 3 5 2.7900 - 2.5900 0.98 1217 133 0.3654 0.4465 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.440 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.030 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 : 0.005 NULL REMARK 3 ANGLE : 1.013 NULL REMARK 3 CHIRALITY : 0.045 164 REMARK 3 PLANARITY : 0.007 33 REMARK 3 DIHEDRAL : 11.738 392 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 9JA7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-SEP-24. REMARK 100 THE DEPOSITION ID IS D_1300050755. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAR-24 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.605 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6866 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.590 REMARK 200 RESOLUTION RANGE LOW (A) : 33.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.4200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.66 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.33700 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: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MOPS (PH7), HEXAMMINE COBALT CHLORIDE, REMARK 280 POTASSIUM CHLORIDE, MPD, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.08600 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 120.17200 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 90.12900 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 150.21500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 30.04300 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 60.08600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 120.17200 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 150.21500 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 90.12900 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 30.04300 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 TOTAL BURIED SURFACE AREA: 260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5860 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 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 K A 107 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 22 O4' REMARK 620 2 C A 22 O2 66.8 REMARK 620 3 G A 25 O6 139.9 145.5 REMARK 620 4 G A 26 O6 136.2 69.4 81.5 REMARK 620 N 1 2 3 DBREF 9JA7 A 1 33 PDB 9JA7 9JA7 1 33 SEQRES 1 A 33 G G C G A U A C C A G C C SEQRES 2 A 33 G A A A G G C C C U U G G SEQRES 3 A 33 C A G C G C C HET NCO A 101 7 HET NCO A 102 7 HET NCO A 103 7 HET NCO A 104 7 HET NCO A 105 7 HET NCO A 106 7 HET K A 107 1 HETNAM NCO COBALT HEXAMMINE(III) HETNAM K POTASSIUM ION FORMUL 2 NCO 6(CO H18 N6 3+) FORMUL 8 K K 1+ FORMUL 9 HOH *(H2 O) LINK O4' C A 22 K K A 107 1555 1555 2.79 LINK O2 C A 22 K K A 107 1555 1555 3.19 LINK O6 G A 25 K K A 107 1555 1555 2.59 LINK O6 G A 26 K K A 107 1555 1555 3.04 CRYST1 46.925 46.925 180.258 90.00 90.00 120.00 P 61 2 2 12 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 0.021311 0.012304 0.000000 0.00000 SCALE2 0.000000 0.024607 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005548 0.00000 TER 705 C A 33 HETATM 706 CO NCO A 101 4.821 -28.914 -0.170 0.69 87.11 CO3+ HETATM 707 N1 NCO A 101 3.631 -29.794 -1.491 0.69 60.80 N HETATM 708 N2 NCO A 101 6.018 -28.023 1.138 0.69 63.45 N HETATM 709 N3 NCO A 101 5.500 -27.754 -1.633 0.69 54.31 N HETATM 710 N4 NCO A 101 6.249 -30.244 -0.532 0.69 60.90 N HETATM 711 N5 NCO A 101 4.109 -30.070 1.270 0.69 65.73 N HETATM 712 N6 NCO A 101 3.405 -27.582 0.205 0.69 67.58 N HETATM 713 CO NCO A 102 4.928 -22.169 3.220 0.90 96.84 CO3+ HETATM 714 N1 NCO A 102 4.707 -24.121 2.934 0.90 69.47 N HETATM 715 N2 NCO A 102 5.134 -20.213 3.489 0.90 62.64 N HETATM 716 N3 NCO A 102 5.616 -21.927 1.374 0.90 62.17 N HETATM 717 N4 NCO A 102 6.778 -22.470 3.869 0.90 65.92 N HETATM 718 N5 NCO A 102 4.268 -22.419 5.073 0.90 60.16 N HETATM 719 N6 NCO A 102 3.070 -21.871 2.581 0.90 72.23 N HETATM 720 CO NCO A 103 -11.434 -26.710 -3.432 0.86 95.44 CO3+ HETATM 721 N1 NCO A 103 -12.005 -28.490 -4.088 0.86 90.97 N HETATM 722 N2 NCO A 103 -10.871 -24.917 -2.778 0.86 68.34 N HETATM 723 N3 NCO A 103 -11.941 -25.907 -5.177 0.86 65.04 N HETATM 724 N4 NCO A 103 -9.609 -27.018 -4.143 0.86 82.01 N HETATM 725 N5 NCO A 103 -10.909 -27.537 -1.708 0.86 68.14 N HETATM 726 N6 NCO A 103 -13.261 -26.423 -2.719 0.86 71.80 N HETATM 727 CO NCO A 104 -5.585 -17.940 24.470 0.83108.02 CO3+ HETATM 728 N1 NCO A 104 -4.327 -19.185 23.575 0.83 85.48 N HETATM 729 N2 NCO A 104 -6.826 -16.693 25.384 0.83 87.25 N HETATM 730 N3 NCO A 104 -4.533 -16.390 23.821 0.83 74.51 N HETATM 731 N4 NCO A 104 -4.468 -18.007 26.105 0.83 93.74 N HETATM 732 N5 NCO A 104 -6.631 -19.490 25.134 0.83 86.00 N HETATM 733 N6 NCO A 104 -6.696 -17.868 22.830 0.83 87.86 N HETATM 734 CO NCO A 105 -4.295 -10.704 18.255 0.74100.79 CO3+ HETATM 735 N1 NCO A 105 -5.498 -12.179 17.705 0.74 84.34 N HETATM 736 N2 NCO A 105 -3.084 -9.235 18.806 0.74 81.95 N HETATM 737 N3 NCO A 105 -5.251 -9.463 17.042 0.74 89.24 N HETATM 738 N4 NCO A 105 -5.530 -10.244 19.740 0.74 79.57 N HETATM 739 N5 NCO A 105 -3.332 -11.937 19.465 0.74 74.27 N HETATM 740 N6 NCO A 105 -3.075 -11.156 16.761 0.74 81.02 N HETATM 741 CO NCO A 106 -1.677 -32.871 4.825 0.79120.26 CO3+ HETATM 742 N1 NCO A 106 -1.023 -34.301 3.615 0.79 95.13 N HETATM 743 N2 NCO A 106 -2.342 -31.444 6.029 0.79101.18 N HETATM 744 N3 NCO A 106 -1.164 -31.502 3.483 0.79 94.84 N HETATM 745 N4 NCO A 106 0.126 -32.728 5.636 0.79 96.18 N HETATM 746 N5 NCO A 106 -2.198 -34.224 6.179 0.79 93.66 N HETATM 747 N6 NCO A 106 -3.483 -33.009 4.019 0.79101.03 N HETATM 748 K K A 107 -6.291 -21.246 4.735 1.00 67.47 K HETATM 749 O HOH A 201 10.085 -24.146 -18.180 1.00 60.38 O CONECT 457 748 CONECT 465 748 CONECT 528 748 CONECT 551 748 CONECT 706 707 708 709 710 CONECT 706 711 712 CONECT 707 706 CONECT 708 706 CONECT 709 706 CONECT 710 706 CONECT 711 706 CONECT 712 706 CONECT 713 714 715 716 717 CONECT 713 718 719 CONECT 714 713 CONECT 715 713 CONECT 716 713 CONECT 717 713 CONECT 718 713 CONECT 719 713 CONECT 720 721 722 723 724 CONECT 720 725 726 CONECT 721 720 CONECT 722 720 CONECT 723 720 CONECT 724 720 CONECT 725 720 CONECT 726 720 CONECT 727 728 729 730 731 CONECT 727 732 733 CONECT 728 727 CONECT 729 727 CONECT 730 727 CONECT 731 727 CONECT 732 727 CONECT 733 727 CONECT 734 735 736 737 738 CONECT 734 739 740 CONECT 735 734 CONECT 736 734 CONECT 737 734 CONECT 738 734 CONECT 739 734 CONECT 740 734 CONECT 741 742 743 744 745 CONECT 741 746 747 CONECT 742 741 CONECT 743 741 CONECT 744 741 CONECT 745 741 CONECT 746 741 CONECT 747 741 CONECT 748 457 465 528 551 MASTER 242 0 7 0 0 0 0 6 748 1 53 3 END