HEADER RNA 10-JUL-18 6E1T TITLE CRYSTAL STRUCTURE OF A CLASS I PREQ1 RIBOSWITCH COMPLEXED WITH A TITLE 2 SYNTHETIC COMPOUND 1: 2-[(DIBENZO[B,D]FURAN-2-YL)OXY]ETHAN-1-AMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (33-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: CALDANAEROBACTER SUBTERRANEUS SUBSP. SOURCE 4 TENGCONGENSIS; SOURCE 5 ORGANISM_TAXID: 119072 KEYWDS PREQ1 RIBOSWITCH, SYNTHETIC COMPOUND, COMPLEX, RNA EXPDTA X-RAY DIFFRACTION AUTHOR T.NUMATA,C.M.CONNELLY,J.S.SCHNEEKLOTH,A.R.FERRE-D'AMARE REVDAT 4 11-OCT-23 6E1T 1 REMARK REVDAT 3 04-DEC-19 6E1T 1 SEQRES REVDAT 2 17-APR-19 6E1T 1 JRNL REVDAT 1 10-APR-19 6E1T 0 JRNL AUTH C.M.CONNELLY,T.NUMATA,R.E.BOER,M.H.MOON,R.S.SINNIAH, JRNL AUTH 2 J.J.BARCHI,A.R.FERRE-D'AMARE,J.S.SCHNEEKLOTH JR. JRNL TITL SYNTHETIC LIGANDS FOR PREQ1RIBOSWITCHES PROVIDE STRUCTURAL JRNL TITL 2 AND MECHANISTIC INSIGHTS INTO TARGETING RNA TERTIARY JRNL TITL 3 STRUCTURE. JRNL REF NAT COMMUN V. 10 1501 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 30940810 JRNL DOI 10.1038/S41467-019-09493-3 REMARK 2 REMARK 2 RESOLUTION. 1.80 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 21663 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1082 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 57.5564 - 3.5999 1.00 2778 145 0.1233 0.1238 REMARK 3 2 3.5999 - 2.8574 1.00 2614 143 0.1697 0.1967 REMARK 3 3 2.8574 - 2.4962 1.00 2585 125 0.2614 0.2819 REMARK 3 4 2.4962 - 2.2680 1.00 2548 132 0.2748 0.2687 REMARK 3 5 2.2680 - 2.1054 0.99 2537 132 0.2847 0.3057 REMARK 3 6 2.1054 - 1.9813 0.99 2530 132 0.3174 0.3123 REMARK 3 7 1.9813 - 1.8820 0.99 2493 142 0.3263 0.3418 REMARK 3 8 1.8820 - 1.8001 0.99 2496 131 0.3676 0.3846 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.49 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.97 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 : 0.005 784 REMARK 3 ANGLE : 0.957 1213 REMARK 3 CHIRALITY : 0.042 158 REMARK 3 PLANARITY : 0.011 31 REMARK 3 DIHEDRAL : 14.950 399 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 1:11) REMARK 3 ORIGIN FOR THE GROUP (A): 40.3368 37.4677 26.2656 REMARK 3 T TENSOR REMARK 3 T11: 0.3734 T22: 0.5442 REMARK 3 T33: 0.3765 T12: 0.1734 REMARK 3 T13: -0.0130 T23: -0.1822 REMARK 3 L TENSOR REMARK 3 L11: 2.3874 L22: 2.1469 REMARK 3 L33: 2.3837 L12: -0.4399 REMARK 3 L13: -2.3847 L23: 0.4993 REMARK 3 S TENSOR REMARK 3 S11: -0.1914 S12: 0.0029 S13: -0.4202 REMARK 3 S21: 0.1229 S22: 0.3706 S23: -0.4327 REMARK 3 S31: 0.2155 S32: 0.4834 S33: -0.0633 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 12:15) REMARK 3 ORIGIN FOR THE GROUP (A): 40.2336 43.4208 19.5297 REMARK 3 T TENSOR REMARK 3 T11: 0.5491 T22: 0.5618 REMARK 3 T33: 0.5156 T12: 0.1518 REMARK 3 T13: 0.0421 T23: -0.1094 REMARK 3 L TENSOR REMARK 3 L11: 3.9321 L22: 5.8953 REMARK 3 L33: 5.1683 L12: 4.6562 REMARK 3 L13: -4.0732 L23: -5.4251 REMARK 3 S TENSOR REMARK 3 S11: -0.7431 S12: 0.2588 S13: 0.1628 REMARK 3 S21: 1.6340 S22: 0.3829 S23: 0.4150 REMARK 3 S31: -0.4615 S32: -1.0181 S33: 0.3706 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 16:33) REMARK 3 ORIGIN FOR THE GROUP (A): 34.3516 37.6221 28.8354 REMARK 3 T TENSOR REMARK 3 T11: 0.3110 T22: 0.4071 REMARK 3 T33: 0.3037 T12: 0.1032 REMARK 3 T13: 0.0278 T23: -0.0662 REMARK 3 L TENSOR REMARK 3 L11: 2.9403 L22: 3.8923 REMARK 3 L33: 5.1119 L12: -2.0128 REMARK 3 L13: -3.4257 L23: 3.0050 REMARK 3 S TENSOR REMARK 3 S11: -0.3079 S12: 0.0545 S13: -0.5094 REMARK 3 S21: 0.2535 S22: 0.0919 S23: -0.0553 REMARK 3 S31: 0.5846 S32: -0.0148 S33: 0.2230 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 6E1T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1000235517. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21704 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 58.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 25.40 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 24.20 REMARK 200 R MERGE FOR SHELL (I) : 2.90600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 2.7.16 REMARK 200 STARTING MODEL: 3Q50 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 76.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.005 M MAGNESIUM ACETATE, 0.05 M MES REMARK 280 (PH 5.6), 2.7 M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 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 REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 -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 0.00000 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 0.00000 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 29.39600 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 29.39600 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 29.39600 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 0.00000 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 0.00000 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 29.39600 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 29.39600 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 29.39600 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 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 MG A 104 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 5 OP2 REMARK 620 2 HOH A 274 O 130.3 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HLV A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 106 DBREF 6E1T A 1 33 PDB 6E1T 6E1T 1 33 SEQRES 1 A 33 C U G G G U C G C A G U N SEQRES 2 A 33 N N C C C A G U U A A C A SEQRES 3 A 33 A A A C A A G HET MES A 101 12 HET HLV A 102 17 HET MG A 103 1 HET MG A 104 1 HET MG A 105 1 HET MG A 106 1 HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM HLV 2-[(DIBENZO[B,D]FURAN-2-YL)OXY]ETHAN-1-AMINE HETNAM MG MAGNESIUM ION FORMUL 2 MES C6 H13 N O4 S FORMUL 3 HLV C14 H13 N O2 FORMUL 4 MG 4(MG 2+) FORMUL 8 HOH *83(H2 O) LINK O3' U A 12 P N A 13 1555 1555 1.61 LINK O3' N A 13 P N A 14 1555 1555 1.61 LINK O3' N A 14 P N A 15 1555 1555 1.61 LINK O3' N A 15 P C A 16 1555 1555 1.60 LINK OP2 G A 5 MG MG A 104 1555 1555 2.33 LINK OP2 C A 7 MG MG A 105 1555 1555 2.20 LINK OP2 A A 10 MG MG A 103 1555 1555 2.48 LINK OP2 A A 28 MG MG A 106 1555 1555 2.43 LINK MG MG A 104 O HOH A 274 1555 1555 2.61 SITE 1 AC1 7 G A 11 U A 12 N A 13 N A 15 SITE 2 AC1 7 A A 31 A A 32 HOH A 258 SITE 1 AC2 10 G A 5 U A 6 C A 7 G A 11 SITE 2 AC2 10 N A 14 N A 15 C A 16 A A 29 SITE 3 AC2 10 MG A 104 HOH A 206 SITE 1 AC3 3 G A 8 C A 9 A A 10 SITE 1 AC4 4 G A 4 G A 5 HLV A 102 HOH A 274 SITE 1 AC5 2 U A 6 C A 7 SITE 1 AC6 3 U A 6 C A 7 A A 28 CRYST1 115.054 115.054 58.792 90.00 90.00 120.00 P 63 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 0.008692 0.005018 0.000000 0.00000 SCALE2 0.000000 0.010036 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017009 0.00000