HEADER RNA 16-FEB-22 7TZR TITLE CRYSTAL STRUCTURE OF THE E. COLI THIM RIBOSWITCH BOUND TO N-METHYL-1- TITLE 2 (QUINOXALIN-6-YL)METHANAMINE (COMPOUND 16) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (80-MER); COMPND 3 CHAIN: X, Y; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 4 ORGANISM_TAXID: 562 KEYWDS THIM TPP RIBOSWITCH, RNA EXPDTA X-RAY DIFFRACTION AUTHOR A.NUTHANAKANTI,A.SERGANOV REVDAT 2 18-OCT-23 7TZR 1 REMARK REVDAT 1 25-MAY-22 7TZR 0 JRNL AUTH M.J.ZELLER,O.FAVOROV,K.LI,A.NUTHANAKANTI,D.HUSSEIN, JRNL AUTH 2 A.MICHAUD,D.A.LAFONTAINE,S.BUSAN,A.SERGANOV,J.AUBE,K.M.WEEKS JRNL TITL SHAPE-ENABLED FRAGMENT-BASED LIGAND DISCOVERY FOR RNA. JRNL REF PROC.NATL.ACAD.SCI.USA V. 119 60119 2022 JRNL REFN ESSN 1091-6490 JRNL PMID 35561226 JRNL DOI 10.1073/PNAS.2122660119 REMARK 2 REMARK 2 RESOLUTION. 2.70 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 11382 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1153 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 29.0500 - 5.3900 0.91 1306 144 0.1666 0.1886 REMARK 3 2 5.3800 - 4.2800 0.95 1294 148 0.1713 0.2291 REMARK 3 3 4.2800 - 3.7400 0.97 1302 150 0.1798 0.2478 REMARK 3 4 3.7400 - 3.4000 0.97 1310 149 0.2086 0.2581 REMARK 3 5 3.4000 - 3.1500 0.97 1316 151 0.2147 0.3018 REMARK 3 6 3.1500 - 2.9700 0.97 1255 138 0.2528 0.3431 REMARK 3 7 2.9700 - 2.8200 0.96 1292 145 0.2796 0.3533 REMARK 3 8 2.8200 - 2.7000 0.88 1154 128 0.3235 0.3888 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) : 0.416 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.987 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.91 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 : 0.003 3826 REMARK 3 ANGLE : 0.848 5962 REMARK 3 CHIRALITY : 0.039 786 REMARK 3 PLANARITY : 0.006 159 REMARK 3 DIHEDRAL : 18.843 1931 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 7TZR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1000263219. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.8-6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9252 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11400 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.15200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.58100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2GDI REMARK 200 REMARK 200 REMARK: SHAPELESS ROD CLUSTER REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TPP RIBOSWITCH RNA (0.2 MM) AND 16 (2 REMARK 280 MM) WERE HEATED IN A BUFFER CONTAINING 50 MM POTASSIUM ACETATE REMARK 280 (PH 6.8) AND 3 (COMPOUND 16) MM MGCL2. RESERVOIR SOLUTION REMARK 280 CONTAINING 0.1 M SODIUM ACETATE (PH 4.8), 0.35 M AMMONIUM REMARK 280 ACETATE, AND 28% (V/V) PEG4000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K 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 75.07800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 14.80400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 75.07800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 14.80400 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: X, Y 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 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 U X 46 O4' C2' O2' C1' N1 C2 O2 REMARK 470 U X 46 N3 C4 O4 C5 C6 REMARK 470 C X 55 N1 C2 O2 N3 C4 N4 C5 REMARK 470 C X 55 C6 REMARK 470 U Y 46 C2 O2 N3 C4 O4 C5 C6 REMARK 470 U Y 54 O4' C2' O2' C1' N1 C2 O2 REMARK 470 U Y 54 N3 C4 O4 C5 C6 REMARK 470 C Y 55 N1 C2 O2 N3 C4 N4 C5 REMARK 470 C Y 55 C6 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 X 103 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G X 21 O2' REMARK 620 2 U X 71 O2' 75.2 REMARK 620 3 U X 71 O2 124.8 76.6 REMARK 620 4 C X 73 OP1 133.2 135.6 99.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG X 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G X 72 O6 REMARK 620 2 G X 78 O6 88.5 REMARK 620 3 HOH X 203 O 63.5 133.9 REMARK 620 N 1 2 DBREF 7TZR X 10 89 PDB 7TZR 7TZR 10 89 DBREF 7TZR Y 10 89 PDB 7TZR 7TZR 10 89 SEQRES 1 X 80 GTP G A C U C G G G G U G C SEQRES 2 X 80 C C U U C U G C G U G A A SEQRES 3 X 80 G G C U G A G A A A U A C SEQRES 4 X 80 C C G U A U C A C C U G A SEQRES 5 X 80 U C U G G A U A A U G C C SEQRES 6 X 80 A G C G U A G G G A A G U SEQRES 7 X 80 U CCC SEQRES 1 Y 80 GTP G A C U C G G G G U G C SEQRES 2 Y 80 C C U U C U G C G U G A A SEQRES 3 Y 80 G G C U G A G A A A U A C SEQRES 4 Y 80 C C G U A U C A C C U G A SEQRES 5 Y 80 U C U G G A U A A U G C C SEQRES 6 Y 80 A G C G U A G G G A A G U SEQRES 7 Y 80 U CCC HET GTP X 10 32 HET CCC X 89 23 HET GTP Y 10 32 HET CCC Y 89 23 HET KWU X 101 24 HET MG X 102 1 HET K X 103 1 HET NA X 104 1 HET KWU Y 101 24 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM CCC CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE HETNAM KWU N-METHYL-1-(QUINOXALIN-6-YL)METHANAMINE HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION HETNAM NA SODIUM ION FORMUL 1 GTP 2(C10 H16 N5 O14 P3) FORMUL 1 CCC 2(C9 H13 N3 O10 P2) FORMUL 3 KWU 2(C10 H11 N3) FORMUL 4 MG MG 2+ FORMUL 5 K K 1+ FORMUL 6 NA NA 1+ FORMUL 8 HOH *34(H2 O) LINK O3' GTP X 10 P G X 11 1555 1555 1.60 LINK O3' U X 88 P CCC X 89 1555 1555 1.61 LINK O3' GTP Y 10 P G Y 11 1555 1555 1.60 LINK O3' U Y 88 P CCC Y 89 1555 1555 1.61 LINK O2' G X 21 K K X 103 1555 1555 2.78 LINK O2' U X 71 K K X 103 1555 1555 2.62 LINK O2 U X 71 K K X 103 1555 1555 3.47 LINK O6 G X 72 MG MG X 102 1555 1555 2.98 LINK OP1 C X 73 K K X 103 1555 1555 2.63 LINK O6 G X 78 MG MG X 102 1555 1555 2.93 LINK MG MG X 102 O HOH X 203 1555 1555 2.85 LINK NA NA X 104 O HOH X 217 1555 1555 2.98 CRYST1 150.156 29.608 95.507 90.00 94.32 90.00 C 1 2 1 8 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 0.006660 0.000000 0.000503 0.00000 SCALE2 0.000000 0.033775 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010500 0.00000 HETATM 1 PG GTP X 10 -26.303 -10.838 -20.487 1.00115.56 P HETATM 2 O1G GTP X 10 -27.234 -11.790 -21.204 1.00 95.19 O HETATM 3 O2G GTP X 10 -26.583 -10.855 -19.002 1.00102.95 O HETATM 4 O3G GTP X 10 -26.504 -9.440 -21.021 1.00104.18 O HETATM 5 O3B GTP X 10 -24.789 -11.334 -20.747 1.00110.59 O HETATM 6 PB GTP X 10 -24.188 -11.441 -22.240 1.00102.17 P HETATM 7 O1B GTP X 10 -25.315 -11.685 -23.217 1.00 84.15 O HETATM 8 O2B GTP X 10 -23.146 -12.534 -22.326 1.00 89.75 O HETATM 9 O3A GTP X 10 -23.529 -9.995 -22.501 1.00 80.51 O HETATM 10 PA GTP X 10 -22.204 -9.574 -21.691 1.00 76.35 P HETATM 11 O1A GTP X 10 -22.203 -10.204 -20.318 1.00 87.11 O HETATM 12 O2A GTP X 10 -22.089 -8.071 -21.610 1.00 75.64 O HETATM 13 O5' GTP X 10 -20.990 -10.189 -22.550 1.00 72.24 O HETATM 14 C5' GTP X 10 -19.949 -9.342 -22.972 1.00 71.01 C HETATM 15 C4' GTP X 10 -19.679 -9.407 -24.471 1.00 69.47 C HETATM 16 O4' GTP X 10 -20.818 -9.659 -25.257 1.00 69.50 O HETATM 17 C3' GTP X 10 -19.232 -8.052 -24.960 1.00 68.36 C HETATM 18 O3' GTP X 10 -17.895 -7.833 -24.583 1.00 69.03 O HETATM 19 C2' GTP X 10 -19.466 -8.066 -26.463 1.00 64.85 C HETATM 20 O2' GTP X 10 -18.434 -8.779 -27.103 1.00 58.60 O HETATM 21 C1' GTP X 10 -20.740 -8.914 -26.464 1.00 66.22 C HETATM 22 N9 GTP X 10 -21.903 -8.009 -26.519 1.00 64.81 N HETATM 23 C8 GTP X 10 -23.036 -8.137 -25.760 1.00 69.72 C HETATM 24 N7 GTP X 10 -23.888 -7.136 -26.071 1.00 66.75 N HETATM 25 C5 GTP X 10 -23.317 -6.372 -27.027 1.00 67.31 C HETATM 26 C6 GTP X 10 -23.763 -5.238 -27.692 1.00 68.43 C HETATM 27 O6 GTP X 10 -24.870 -4.767 -27.434 1.00 69.77 O HETATM 28 N1 GTP X 10 -22.962 -4.650 -28.648 1.00 62.67 N HETATM 29 C2 GTP X 10 -21.728 -5.193 -28.934 1.00 63.55 C HETATM 30 N2 GTP X 10 -20.959 -4.616 -29.853 1.00 67.03 N HETATM 31 N3 GTP X 10 -21.288 -6.321 -28.266 1.00 66.87 N HETATM 32 C4 GTP X 10 -22.070 -6.907 -27.325 1.00 64.92 C