HEADER RNA 19-JAN-24 8VQV TITLE STRUCTURE OF S. ODONTOLYTICA ZTP RIBOSWITCH BOUND TO M-1-PYRIDINYL- TITLE 2 AICA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (64-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHAALIA ODONTOLYTICA; SOURCE 3 ORGANISM_TAXID: 1660; SOURCE 4 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-TP(DELTAI); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 905931 KEYWDS RIBOSWITCH, DRUG, SYNTHETIC, APTAMER, RNA EXPDTA X-RAY DIFFRACTION AUTHOR C.P.JONES,A.R.FERRE D'AMARE REVDAT 2 06-AUG-25 8VQV 1 JRNL REVDAT 1 11-JUN-25 8VQV 0 JRNL AUTH C.R.FULLENKAMP,S.MEHDI,C.P.JONES,L.TENNEY,P.PICHLING, JRNL AUTH 2 P.R.PRESTWOOD,A.R.FERRE-D'AMARE,P.TIWARY,J.S.SCHNEEKLOTH JRNL TITL MACHINE LEARNING-AUGMENTED MOLECULAR DYNAMICS SIMULATIONS JRNL TITL 2 (MD) REVEAL INSIGHTS INTO THE DISCONNECT BETWEEN AFFINITY JRNL TITL 3 AND ACTIVATION OF ZTP RIBOSWITCH LIGANDS. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 64 05971 2025 JRNL REFN ESSN 1521-3773 JRNL PMID 40310613 JRNL DOI 10.1002/ANIE.202505971 REMARK 2 REMARK 2 RESOLUTION. 2.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19.2_4158: ???) 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) : 2.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 14549 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1448 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 40.4400 - 5.2300 1.00 1304 151 0.1472 0.2000 REMARK 3 2 5.2300 - 4.1500 1.00 1311 135 0.1696 0.2040 REMARK 3 3 4.1500 - 3.6300 1.00 1332 144 0.1994 0.2507 REMARK 3 4 3.6300 - 3.3000 1.00 1321 143 0.1968 0.2374 REMARK 3 5 3.3000 - 3.0600 1.00 1298 143 0.2120 0.2722 REMARK 3 6 3.0600 - 2.8800 1.00 1313 147 0.2920 0.3850 REMARK 3 7 2.8800 - 2.7400 1.00 1300 140 0.3128 0.3766 REMARK 3 8 2.7400 - 2.6200 1.00 1320 153 0.3475 0.3206 REMARK 3 9 2.6200 - 2.5200 1.00 1307 148 0.3790 0.3647 REMARK 3 10 2.5200 - 2.4300 1.00 1295 144 0.4953 0.5558 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) : 0.490 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.280 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 1562 REMARK 3 ANGLE : 1.073 2440 REMARK 3 CHIRALITY : 0.041 319 REMARK 3 PLANARITY : 0.006 67 REMARK 3 DIHEDRAL : 14.650 766 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 20 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.7525 -3.0186 -17.6655 REMARK 3 T TENSOR REMARK 3 T11: 0.6068 T22: 0.5653 REMARK 3 T33: 0.5175 T12: -0.0125 REMARK 3 T13: -0.1398 T23: 0.0132 REMARK 3 L TENSOR REMARK 3 L11: 2.0149 L22: 3.7085 REMARK 3 L33: 2.7772 L12: -0.1541 REMARK 3 L13: -0.6723 L23: 0.0554 REMARK 3 S TENSOR REMARK 3 S11: 0.1079 S12: 0.1599 S13: -0.1906 REMARK 3 S21: 0.1867 S22: -0.2908 S23: -0.2344 REMARK 3 S31: -0.0420 S32: 0.3352 S33: 0.2094 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 21 THROUGH 45 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.7307 -6.9515 -16.9506 REMARK 3 T TENSOR REMARK 3 T11: 0.5414 T22: 0.5070 REMARK 3 T33: 0.6245 T12: 0.0738 REMARK 3 T13: -0.1004 T23: -0.0244 REMARK 3 L TENSOR REMARK 3 L11: 1.7222 L22: 4.4784 REMARK 3 L33: 2.7813 L12: 0.0400 REMARK 3 L13: -1.0869 L23: -0.0748 REMARK 3 S TENSOR REMARK 3 S11: -0.0580 S12: 0.0592 S13: -0.6513 REMARK 3 S21: 0.1690 S22: -0.0963 S23: 0.7766 REMARK 3 S31: 0.1919 S32: -0.2502 S33: 0.1390 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 46 THROUGH 64 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.2278 -24.6410 6.6367 REMARK 3 T TENSOR REMARK 3 T11: 0.5325 T22: 1.1888 REMARK 3 T33: 0.6362 T12: -0.0197 REMARK 3 T13: -0.0888 T23: 0.2565 REMARK 3 L TENSOR REMARK 3 L11: 0.4231 L22: 0.6918 REMARK 3 L33: 2.4301 L12: -0.0420 REMARK 3 L13: -0.6269 L23: 1.0482 REMARK 3 S TENSOR REMARK 3 S11: -0.0154 S12: 1.6926 S13: 0.8024 REMARK 3 S21: -0.2802 S22: -0.0743 S23: 0.2102 REMARK 3 S31: -0.1280 S32: 0.1165 S33: 0.0542 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 8VQV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1000280506. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-21 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 : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.105030 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14549 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.430 REMARK 200 RESOLUTION RANGE LOW (A) : 40.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 12.00 REMARK 200 R MERGE (I) : 0.09664 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.2700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.52 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: MOLECULAR REPLACEMENT 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 (%): 48.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TBD, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 118.69900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 20.51750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 20.51750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 178.04850 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 20.51750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 20.51750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 59.34950 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 20.51750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.51750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 178.04850 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 20.51750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.51750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 59.34950 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 118.69900 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -68.0 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 MG A 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 11 OP1 REMARK 620 2 C A 29 OP2 173.6 REMARK 620 3 UG4 A 103 O06 22.0 154.5 REMARK 620 4 HOH A 207 O 19.5 156.6 3.0 REMARK 620 5 HOH A 213 O 23.6 152.4 2.9 4.2 REMARK 620 6 HOH A 215 O 22.1 153.4 4.7 3.8 2.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 204 O REMARK 620 2 HOH A 212 O 91.5 REMARK 620 3 HOH A 217 O 90.1 178.5 REMARK 620 4 HOH A 218 O 90.7 91.0 89.0 REMARK 620 5 HOH A 222 O 88.0 88.5 91.6 178.6 REMARK 620 6 HOH A 223 O 179.6 88.8 89.7 89.6 91.6 REMARK 620 N 1 2 3 4 5 DBREF 8VQV A 1 64 PDB 8VQV 8VQV 1 64 SEQRES 1 A 64 G G G U C G U G A C U G G SEQRES 2 A 64 C G A A C A G G U G G G A SEQRES 3 A 64 A A C C A C C G G G G A G SEQRES 4 A 64 C G A C C C U U G C C G C SEQRES 5 A 64 C C G C C U G G G C A A HET MG A 101 1 HET MG A 102 1 HET UG4 A 103 15 HETNAM MG MAGNESIUM ION HETNAM UG4 5-AMINO-1-(PYRIDIN-3-YL)-1H-IMIDAZOLE-4-CARBOXAMIDE FORMUL 2 MG 2(MG 2+) FORMUL 4 UG4 C9 H9 N5 O FORMUL 5 HOH *23(H2 O) LINK OP1 U A 11 MG MG A 101 1555 7555 2.07 LINK OP2 C A 29 MG MG A 101 1555 7555 1.93 LINK MG MG A 101 O06 UG4 A 103 1555 1555 2.07 LINK MG MG A 101 O HOH A 207 1555 1555 2.24 LINK MG MG A 101 O HOH A 213 1555 1555 2.02 LINK MG MG A 101 O HOH A 215 1555 7555 2.29 LINK MG MG A 102 O HOH A 204 1555 1555 2.18 LINK MG MG A 102 O HOH A 212 1555 1555 2.19 LINK MG MG A 102 O HOH A 217 1555 1555 2.19 LINK MG MG A 102 O HOH A 218 1555 1555 2.18 LINK MG MG A 102 O HOH A 222 1555 1555 2.18 LINK MG MG A 102 O HOH A 223 1555 1555 2.18 CRYST1 41.035 41.035 237.398 90.00 90.00 90.00 P 43 21 2 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 0.024369 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024369 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004212 0.00000 CONECT 1378 1394 1401 1407 CONECT 1379 1398 1406 1411 1412 CONECT 1379 1416 1417 CONECT 1380 1383 1388 1393 CONECT 1381 1382 1388 CONECT 1382 1381 1389 CONECT 1383 1380 1389 CONECT 1384 1385 1390 1393 CONECT 1385 1384 1386 1392 CONECT 1386 1385 1391 1394 CONECT 1387 1392 1393 CONECT 1388 1380 1381 CONECT 1389 1382 1383 CONECT 1390 1384 CONECT 1391 1386 CONECT 1392 1385 1387 CONECT 1393 1380 1384 1387 CONECT 1394 1378 1386 CONECT 1398 1379 CONECT 1401 1378 CONECT 1406 1379 CONECT 1407 1378 CONECT 1411 1379 CONECT 1412 1379 CONECT 1416 1379 CONECT 1417 1379 MASTER 291 0 3 0 0 0 0 6 1416 1 26 5 END