HEADER RNA 10-JUL-18 6E1U TITLE CRYSTAL STRUCTURE OF A CLASS I PREQ1 RIBOSWITCH COMPLEXED WITH A TITLE 2 SYNTHETIC COMPOUND 2: 2-[(DIBENZO[B,D]FURAN-2-YL)OXY]-N,N- TITLE 3 DIMETHYLETHAN-1-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 6E1U 1 REMARK REVDAT 3 04-DEC-19 6E1U 1 SEQRES REVDAT 2 17-APR-19 6E1U 1 JRNL REVDAT 1 10-APR-19 6E1U 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. 1.94 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) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 17448 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 869 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 57.7060 - 3.5251 1.00 2949 155 0.1335 0.1447 REMARK 3 2 3.5251 - 2.7979 1.00 2777 143 0.1805 0.1889 REMARK 3 3 2.7979 - 2.4443 1.00 2725 147 0.2855 0.3482 REMARK 3 4 2.4443 - 2.2208 1.00 2703 158 0.2782 0.2658 REMARK 3 5 2.2208 - 2.0616 1.00 2730 121 0.3334 0.3300 REMARK 3 6 2.0616 - 1.9400 1.00 2695 145 0.3769 0.4046 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.84 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 : 0.004 773 REMARK 3 ANGLE : 1.059 1197 REMARK 3 CHIRALITY : 0.044 157 REMARK 3 PLANARITY : 0.011 32 REMARK 3 DIHEDRAL : 16.378 380 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): 40.4570 37.5763 26.0691 REMARK 3 T TENSOR REMARK 3 T11: 0.4765 T22: 0.6908 REMARK 3 T33: 0.4607 T12: 0.2200 REMARK 3 T13: 0.0074 T23: -0.1737 REMARK 3 L TENSOR REMARK 3 L11: 1.9387 L22: 2.6140 REMARK 3 L33: 5.8498 L12: 1.3031 REMARK 3 L13: -1.7202 L23: 1.5908 REMARK 3 S TENSOR REMARK 3 S11: -0.0269 S12: 0.1669 S13: -0.3953 REMARK 3 S21: 0.1725 S22: 0.3495 S23: -0.7109 REMARK 3 S31: 0.2921 S32: 0.3311 S33: -0.2992 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 12:15) REMARK 3 ORIGIN FOR THE GROUP (A): 38.7663 43.9959 17.9510 REMARK 3 T TENSOR REMARK 3 T11: 0.7514 T22: 0.9550 REMARK 3 T33: 1.1107 T12: 0.1103 REMARK 3 T13: 0.0695 T23: 0.0742 REMARK 3 L TENSOR REMARK 3 L11: 1.1899 L22: 4.3039 REMARK 3 L33: 7.3603 L12: -0.7712 REMARK 3 L13: 2.4495 L23: -4.5608 REMARK 3 S TENSOR REMARK 3 S11: -0.3317 S12: -0.1838 S13: 2.7363 REMARK 3 S21: 1.6061 S22: 2.0317 S23: 2.2220 REMARK 3 S31: -0.1704 S32: -2.0385 S33: -1.7458 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 16:33) REMARK 3 ORIGIN FOR THE GROUP (A): 34.5501 37.6583 28.6475 REMARK 3 T TENSOR REMARK 3 T11: 0.3968 T22: 0.5850 REMARK 3 T33: 0.4201 T12: 0.1290 REMARK 3 T13: 0.0105 T23: -0.0994 REMARK 3 L TENSOR REMARK 3 L11: 2.0260 L22: 5.1087 REMARK 3 L33: 8.3874 L12: -0.9987 REMARK 3 L13: -3.1236 L23: 2.7708 REMARK 3 S TENSOR REMARK 3 S11: -0.2558 S12: 0.1488 S13: -0.5778 REMARK 3 S21: 0.3204 S22: -0.0419 S23: -0.0564 REMARK 3 S31: 0.9977 S32: -0.1002 S33: 0.2722 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 6E1U 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_1000235531. 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 : 17502 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.940 REMARK 200 RESOLUTION RANGE LOW (A) : 99.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 25.60 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 26.80 REMARK 200 R MERGE FOR SHELL (I) : 4.30300 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: 0.2 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 29.23150 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 29.23150 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 29.23150 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 29.23150 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 29.23150 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 29.23150 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 221 LIES ON A SPECIAL POSITION. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HMJ A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 102 DBREF 6E1U A 1 33 PDB 6E1U 6E1U 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 HMJ A 101 19 HET MG A 102 1 HETNAM HMJ 2-[(DIBENZO[B,D]FURAN-2-YL)OXY]-N,N-DIMETHYLETHAN-1- HETNAM 2 HMJ AMINE HETNAM MG MAGNESIUM ION FORMUL 2 HMJ C16 H17 N O2 FORMUL 3 MG MG 2+ FORMUL 4 HOH *50(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 LINK OP2 G A 3 MG MG A 102 1555 1555 2.46 SITE 1 AC1 7 G A 5 U A 6 C A 7 G A 11 SITE 2 AC1 7 C A 15 C A 16 A A 29 SITE 1 AC2 2 G A 3 G A 4 CRYST1 115.361 115.361 58.463 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 0.008668 0.005005 0.000000 0.00000 SCALE2 0.000000 0.010009 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017105 0.00000