HEADER RNA 10-JUL-18 6E1V TITLE CRYSTAL STRUCTURE OF A CLASS I PREQ1 RIBOSWITCH COMPLEXED WITH A TITLE 2 SYNTHETIC COMPOUND 3: 2-[(9H-CARBAZOL-3-YL)OXY]-N,N-DIMETHYLETHAN-1- TITLE 3 AMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (33-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: 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 6E1V 1 REMARK REVDAT 3 04-DEC-19 6E1V 1 SEQRES REVDAT 2 17-APR-19 6E1V 1 JRNL REVDAT 1 10-APR-19 6E1V 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. 2.56 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) : 2.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 7764 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.239 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 389 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 41.0970 - 3.6918 0.99 2573 137 0.2033 0.2087 REMARK 3 2 3.6918 - 2.9305 0.99 2401 127 0.2423 0.2702 REMARK 3 3 2.9305 - 2.5602 0.99 2401 125 0.4625 0.4636 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) : 0.540 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 66.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 79.88 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 : 0.005 774 REMARK 3 ANGLE : 0.965 1200 REMARK 3 CHIRALITY : 0.046 158 REMARK 3 PLANARITY : 0.010 31 REMARK 3 DIHEDRAL : 16.708 389 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): 40.1087 37.4894 26.8441 REMARK 3 T TENSOR REMARK 3 T11: 0.7620 T22: 1.0933 REMARK 3 T33: 1.2689 T12: 0.2764 REMARK 3 T13: 0.1785 T23: -0.8360 REMARK 3 L TENSOR REMARK 3 L11: 0.5331 L22: 0.5614 REMARK 3 L33: 1.7817 L12: -0.3921 REMARK 3 L13: -0.7698 L23: 0.9951 REMARK 3 S TENSOR REMARK 3 S11: 0.2171 S12: 0.1148 S13: -0.1312 REMARK 3 S21: -0.0308 S22: 0.1431 S23: -0.2304 REMARK 3 S31: -0.1890 S32: 0.1513 S33: 0.0317 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 11:15) REMARK 3 ORIGIN FOR THE GROUP (A): 40.8493 41.4243 19.7698 REMARK 3 T TENSOR REMARK 3 T11: 0.9390 T22: 1.0362 REMARK 3 T33: 1.0730 T12: 0.1380 REMARK 3 T13: 0.2197 T23: -0.5695 REMARK 3 L TENSOR REMARK 3 L11: 0.0175 L22: 3.8728 REMARK 3 L33: 0.4307 L12: -0.1561 REMARK 3 L13: 0.0862 L23: -0.6359 REMARK 3 S TENSOR REMARK 3 S11: -0.0374 S12: -0.0970 S13: 0.1901 REMARK 3 S21: 0.7540 S22: 0.0270 S23: 0.4968 REMARK 3 S31: -0.7007 S32: -0.5774 S33: -0.1430 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 16:33) REMARK 3 ORIGIN FOR THE GROUP (A): 34.4995 37.5398 28.8423 REMARK 3 T TENSOR REMARK 3 T11: 0.7009 T22: 0.8980 REMARK 3 T33: 0.8413 T12: 0.1297 REMARK 3 T13: 0.0105 T23: -0.5526 REMARK 3 L TENSOR REMARK 3 L11: 1.2178 L22: 2.2063 REMARK 3 L33: 5.1654 L12: -1.4412 REMARK 3 L13: -2.4167 L23: 2.4342 REMARK 3 S TENSOR REMARK 3 S11: 0.0309 S12: 0.0145 S13: -0.3554 REMARK 3 S21: 0.0150 S22: 0.2255 S23: -0.4531 REMARK 3 S31: 0.2197 S32: 0.2897 S33: 0.1314 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 6E1V 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_1000235532. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-FEB-18 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 : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97741 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.6.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7832 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.560 REMARK 200 RESOLUTION RANGE LOW (A) : 41.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 37.70 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 29.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 38.20 REMARK 200 R MERGE FOR SHELL (I) : 1.85300 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): 5.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M POTASSIUM SODIUM TARTRATE, 0.1 M REMARK 280 SODIUM CITRATE (PH 5.6), 2.8 M AMMONIUM SULFATE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, 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 29.26150 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 29.26150 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 29.26150 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 29.26150 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 29.26150 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 29.26150 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 N A 14 C5' C2' REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HMV A 101 DBREF 6E1V A 1 33 PDB 6E1V 6E1V 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 HMV A 101 19 HETNAM HMV 2-[(9H-CARBAZOL-3-YL)OXY]-N,N-DIMETHYLETHAN-1-AMINE FORMUL 2 HMV C16 H18 N2 O FORMUL 3 HOH *2(H2 O) LINK O3' U A 12 P N A 13 1555 1555 1.60 LINK O3' N A 13 P N A 14 1555 1555 1.61 LINK O3' N A 14 P N A 15 1555 1555 1.62 LINK O3' N A 15 P C A 16 1555 1555 1.62 SITE 1 AC1 7 G A 5 U A 6 C A 7 G A 11 SITE 2 AC1 7 N A 14 C A 16 A A 29 CRYST1 115.421 115.421 58.523 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 0.008664 0.005002 0.000000 0.00000 SCALE2 0.000000 0.010004 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017087 0.00000