HEADER RNA 10-JUL-18 6E1W TITLE CRYSTAL STRUCTURE OF A CLASS I PREQ1 RIBOSWITCH COMPLEXED WITH PREQ1 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 13-MAR-24 6E1W 1 LINK REVDAT 3 04-DEC-19 6E1W 1 SEQRES REVDAT 2 17-APR-19 6E1W 1 JRNL REVDAT 1 10-APR-19 6E1W 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. 1.69 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) : 1.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 17086 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 854 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 43.9249 - 3.0707 1.00 2946 156 0.1416 0.1735 REMARK 3 2 3.0707 - 2.4373 1.00 2748 143 0.2369 0.2516 REMARK 3 3 2.4373 - 2.1293 1.00 2698 143 0.2462 0.3180 REMARK 3 4 2.1293 - 1.9346 1.00 2653 139 0.2461 0.2555 REMARK 3 5 1.9346 - 1.7959 1.00 2636 139 0.2514 0.2784 REMARK 3 6 1.7959 - 1.6900 0.97 2551 134 0.2646 0.2701 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.17 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 : 0.005 773 REMARK 3 ANGLE : 0.989 1197 REMARK 3 CHIRALITY : 0.046 157 REMARK 3 PLANARITY : 0.012 34 REMARK 3 DIHEDRAL : 13.066 379 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 1:8) REMARK 3 ORIGIN FOR THE GROUP (A): 37.6668 38.2491 30.0324 REMARK 3 T TENSOR REMARK 3 T11: 0.4020 T22: 0.5163 REMARK 3 T33: 0.3782 T12: 0.1578 REMARK 3 T13: 0.0679 T23: 0.0296 REMARK 3 L TENSOR REMARK 3 L11: 0.8696 L22: 7.8961 REMARK 3 L33: 4.6023 L12: -2.0799 REMARK 3 L13: 1.1068 L23: 0.4207 REMARK 3 S TENSOR REMARK 3 S11: -0.1043 S12: -0.0033 S13: 0.0717 REMARK 3 S21: 0.2522 S22: 0.1695 S23: -0.5614 REMARK 3 S31: 0.7055 S32: 0.3837 S33: -0.0550 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 9:16) REMARK 3 ORIGIN FOR THE GROUP (A): 38.2530 34.8162 20.0569 REMARK 3 T TENSOR REMARK 3 T11: 0.5225 T22: 0.3926 REMARK 3 T33: 0.4491 T12: 0.0778 REMARK 3 T13: 0.0597 T23: -0.0385 REMARK 3 L TENSOR REMARK 3 L11: 2.9242 L22: 9.6377 REMARK 3 L33: 6.5778 L12: 0.8423 REMARK 3 L13: 1.5817 L23: 2.4931 REMARK 3 S TENSOR REMARK 3 S11: -0.0044 S12: 0.1079 S13: 0.9372 REMARK 3 S21: -0.3537 S22: -0.0113 S23: -0.6283 REMARK 3 S31: -0.0844 S32: 0.3245 S33: -0.0348 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 17:23) REMARK 3 ORIGIN FOR THE GROUP (A): 32.1170 45.0929 36.3141 REMARK 3 T TENSOR REMARK 3 T11: 0.3583 T22: 0.5416 REMARK 3 T33: 0.3852 T12: 0.0858 REMARK 3 T13: 0.0474 T23: -0.0270 REMARK 3 L TENSOR REMARK 3 L11: 8.3478 L22: 2.2386 REMARK 3 L33: 2.5224 L12: 3.5122 REMARK 3 L13: 2.9978 L23: 0.7650 REMARK 3 S TENSOR REMARK 3 S11: -0.0254 S12: -0.3598 S13: -0.0336 REMARK 3 S21: 0.2219 S22: -0.2430 S23: 0.1811 REMARK 3 S31: 0.3594 S32: 0.0125 S33: 0.2448 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 24:33) REMARK 3 ORIGIN FOR THE GROUP (A): 34.3148 30.6623 26.7568 REMARK 3 T TENSOR REMARK 3 T11: 0.5622 T22: 0.3584 REMARK 3 T33: 0.3933 T12: 0.0631 REMARK 3 T13: 0.0458 T23: 0.0080 REMARK 3 L TENSOR REMARK 3 L11: 3.6764 L22: 8.3403 REMARK 3 L33: 4.4818 L12: -2.1123 REMARK 3 L13: -1.8575 L23: 6.0935 REMARK 3 S TENSOR REMARK 3 S11: -0.1627 S12: -0.0950 S13: -0.2124 REMARK 3 S21: 0.6937 S22: -0.1665 S23: 0.5348 REMARK 3 S31: 1.3995 S32: -0.0957 S33: 0.4239 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 6E1W 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_1000235535. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-SEP-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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17169 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 REMARK 200 RESOLUTION RANGE LOW (A) : 44.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 33.20 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 44.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : 19.00 REMARK 200 R MERGE FOR SHELL (I) : 1.41100 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 2.7.16 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01 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 61 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 59.73833 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 119.47667 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 89.60750 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 149.34583 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 29.86917 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 59.73833 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 119.47667 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 149.34583 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 89.60750 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 29.86917 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 A A 31 OP2 REMARK 620 2 HOH A 274 O 123.7 REMARK 620 3 HOH A 277 O 126.6 91.8 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HNG A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT 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 DBREF 6E1W A 1 33 PDB 6E1W 6E1W 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 HNG A 101 13 HET ACT A 102 4 HET ACT A 103 4 HET MG A 104 1 HETNAM HNG 2-AMINO-5-(AMINOMETHYL)-1,7-DIHYDRO-4H-PYRROLO[2,3- HETNAM 2 HNG D]PYRIMIDIN-4-ONE HETNAM ACT ACETATE ION HETNAM MG MAGNESIUM ION HETSYN HNG PREQ1 FORMUL 2 HNG C7 H9 N5 O FORMUL 3 ACT 2(C2 H3 O2 1-) FORMUL 5 MG MG 2+ FORMUL 6 HOH *96(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 C A 15 1555 1555 1.62 LINK OP2 A A 31 MG MG A 104 1555 1555 2.17 LINK MG MG A 104 O HOH A 274 1555 1555 2.61 LINK MG MG A 104 O HOH A 277 1555 1555 2.58 SITE 1 AC1 9 G A 5 U A 6 C A 7 G A 11 SITE 2 AC1 9 C A 15 C A 16 A A 29 C A 30 SITE 3 AC1 9 ACT A 102 SITE 1 AC2 4 G A 11 HNG A 101 HOH A 242 HOH A 273 SITE 1 AC3 5 C A 9 HOH A 217 HOH A 234 HOH A 277 SITE 2 AC3 5 HOH A 288 SITE 1 AC4 4 C A 30 A A 31 HOH A 274 HOH A 277 CRYST1 52.297 52.297 179.215 90.00 90.00 120.00 P 61 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 0.019122 0.011040 0.000000 0.00000 SCALE2 0.000000 0.022080 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005580 0.00000