HEADER RNA 10-JUL-18 6E1S 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 6E1S 1 REMARK REVDAT 3 04-DEC-19 6E1S 1 SEQRES REVDAT 2 17-APR-19 6E1S 1 JRNL REVDAT 1 10-APR-19 6E1S 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 21838 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.197 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 : 1090 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 57.7271 - 3.5999 1.00 2790 147 0.1309 0.1214 REMARK 3 2 3.5999 - 2.8574 1.00 2634 143 0.1662 0.1992 REMARK 3 3 2.8574 - 2.4962 1.00 2603 125 0.2741 0.2911 REMARK 3 4 2.4962 - 2.2679 1.00 2557 138 0.2706 0.2455 REMARK 3 5 2.2679 - 2.1054 1.00 2565 133 0.2928 0.3743 REMARK 3 6 2.1054 - 1.9812 1.00 2560 133 0.3294 0.3125 REMARK 3 7 1.9812 - 1.8820 1.00 2526 141 0.3456 0.3963 REMARK 3 8 1.8820 - 1.8001 0.99 2513 130 0.4055 0.4228 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.870 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.49 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 : 0.005 771 REMARK 3 ANGLE : 0.930 1194 REMARK 3 CHIRALITY : 0.042 157 REMARK 3 PLANARITY : 0.011 32 REMARK 3 DIHEDRAL : 13.665 381 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 1:10) REMARK 3 ORIGIN FOR THE GROUP (A): 40.2860 37.8051 26.8769 REMARK 3 T TENSOR REMARK 3 T11: 0.4389 T22: 0.6097 REMARK 3 T33: 0.3643 T12: 0.2357 REMARK 3 T13: 0.0095 T23: -0.1536 REMARK 3 L TENSOR REMARK 3 L11: 1.7573 L22: 1.7682 REMARK 3 L33: 0.8244 L12: 0.9996 REMARK 3 L13: -0.9602 L23: 0.0547 REMARK 3 S TENSOR REMARK 3 S11: 0.0282 S12: 0.0535 S13: -0.3136 REMARK 3 S21: -0.0556 S22: 0.2560 S23: -0.6900 REMARK 3 S31: 0.1096 S32: 0.3090 S33: -0.1963 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 11:15) REMARK 3 ORIGIN FOR THE GROUP (A): 39.8010 41.5947 18.7689 REMARK 3 T TENSOR REMARK 3 T11: 0.3373 T22: 0.5733 REMARK 3 T33: 0.6339 T12: 0.2233 REMARK 3 T13: 0.0765 T23: -0.1605 REMARK 3 L TENSOR REMARK 3 L11: 3.0100 L22: 0.3509 REMARK 3 L33: 2.5446 L12: 0.9987 REMARK 3 L13: 0.6324 L23: 0.4293 REMARK 3 S TENSOR REMARK 3 S11: -0.4039 S12: 0.1050 S13: 0.8263 REMARK 3 S21: 0.8528 S22: 0.5203 S23: 0.7839 REMARK 3 S31: -0.5306 S32: -0.6270 S33: -0.3352 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 16:33) REMARK 3 ORIGIN FOR THE GROUP (A): 34.5063 37.7111 28.8276 REMARK 3 T TENSOR REMARK 3 T11: 0.2978 T22: 0.4676 REMARK 3 T33: 0.3247 T12: 0.1256 REMARK 3 T13: 0.0228 T23: -0.0690 REMARK 3 L TENSOR REMARK 3 L11: 1.7461 L22: 3.6924 REMARK 3 L33: 8.8102 L12: -0.9377 REMARK 3 L13: -2.9086 L23: 2.7560 REMARK 3 S TENSOR REMARK 3 S11: -0.2876 S12: -0.0379 S13: -0.4247 REMARK 3 S21: 0.2749 S22: 0.0544 S23: -0.0586 REMARK 3 S31: 0.7443 S32: -0.0543 S33: 0.2172 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 6E1S 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_1000235503. 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 : 21898 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 57.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 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 : 15.7000 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 24.00 REMARK 200 R MERGE FOR SHELL (I) : 4.30200 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 (%): 76.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01 M MAGNESIUM ACETATE, 0.05 M MES REMARK 280 (PH 5.6), 2.6 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 29.39200 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 29.39200 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 29.39200 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 29.39200 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 29.39200 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 29.39200 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HLV A 101 DBREF 6E1S A 1 33 PDB 6E1S 6E1S 1 33 SEQRES 1 A 33 C U G G G U C G C A G U N SEQRES 2 A 33 N C C C C A G U U A A C A SEQRES 3 A 33 A A A C A A G HET HLV A 101 17 HETNAM HLV 2-[(DIBENZO[B,D]FURAN-2-YL)OXY]ETHAN-1-AMINE FORMUL 2 HLV C14 H13 N O2 FORMUL 3 HOH *66(H2 O) LINK O3' U A 12 P N A 13 1555 1555 1.61 LINK O3' N A 14 P C A 15 1555 1555 1.61 SITE 1 AC1 8 G A 5 U A 6 C A 7 G A 11 SITE 2 AC1 8 C A 15 C A 16 A A 29 HOH A 214 CRYST1 115.395 115.395 58.784 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 0.008666 0.005003 0.000000 0.00000 SCALE2 0.000000 0.010007 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017012 0.00000