HEADER RNA 02-JUN-18 6DLR TITLE PRPP RIBOSWITCH BOUND TO PRPP, IRIDIUM-HEXAMINE SOAKED STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRPP RIBOSWITCH; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTROPHOTHERMUS LIPOCALIDUS DSM 12680; SOURCE 3 ORGANISM_TAXID: 643648; SOURCE 4 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-TP(DELTAI); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 905931; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PUT7 KEYWDS RIBOSWITCH, NON-CODING, RNA, YKKC EXPDTA X-RAY DIFFRACTION AUTHOR A.PESELIS,A.SERGANOV REVDAT 4 27-APR-22 6DLR 1 SPRSDE HETSYN REVDAT 3 29-JUL-20 6DLR 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 01-JAN-20 6DLR 1 SPRSDE REVDAT 1 14-NOV-18 6DLR 0 JRNL AUTH A.PESELIS,A.SERGANOV JRNL TITL YKKC RIBOSWITCHES EMPLOY AN ADD-ON HELIX TO ADJUST JRNL TITL 2 SPECIFICITY FOR POLYANIONIC LIGANDS. JRNL REF NAT. CHEM. BIOL. V. 14 887 2018 JRNL REFN ESSN 1552-4469 JRNL PMID 30120360 JRNL DOI 10.1038/S41589-018-0114-4 REMARK 2 REMARK 2 RESOLUTION. 2.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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) : 2.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.8 REMARK 3 NUMBER OF REFLECTIONS : 24713 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.910 REMARK 3 FREE R VALUE TEST SET COUNT : 2449 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 19.5358 - 6.7406 0.88 1292 137 0.1936 0.1949 REMARK 3 2 6.7406 - 5.3872 0.91 1330 154 0.1626 0.1799 REMARK 3 3 5.3872 - 4.7172 0.96 1412 152 0.1600 0.1808 REMARK 3 4 4.7172 - 4.2909 0.95 1391 153 0.1712 0.2066 REMARK 3 5 4.2909 - 3.9861 0.90 1300 157 0.1740 0.1734 REMARK 3 6 3.9861 - 3.7528 0.94 1351 153 0.1770 0.1696 REMARK 3 7 3.7528 - 3.5661 0.96 1410 146 0.1765 0.2648 REMARK 3 8 3.5661 - 3.4117 0.96 1397 144 0.1995 0.2423 REMARK 3 9 3.4117 - 3.2810 0.96 1391 154 0.1894 0.2470 REMARK 3 10 3.2810 - 3.1683 0.92 1374 154 0.2153 0.2686 REMARK 3 11 3.1683 - 3.0696 0.91 1324 146 0.2673 0.2671 REMARK 3 12 3.0696 - 2.9822 0.94 1312 145 0.2688 0.2875 REMARK 3 13 2.9822 - 2.9039 0.93 1381 166 0.2785 0.3272 REMARK 3 14 2.9039 - 2.8333 0.91 1335 124 0.3096 0.3639 REMARK 3 15 2.8333 - 2.7690 0.86 1289 134 0.3413 0.3690 REMARK 3 16 2.7690 - 2.7103 0.81 1144 138 0.3387 0.3844 REMARK 3 17 2.7103 - 2.6562 0.56 831 92 0.3558 0.3969 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.590 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.002 2708 REMARK 3 ANGLE : 0.551 4326 REMARK 3 CHIRALITY : 0.025 538 REMARK 3 PLANARITY : 0.003 109 REMARK 3 DIHEDRAL : 14.936 1293 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6DLR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000234722. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-AUG-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1051 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24713 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.11900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.56300 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: NULL REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M NH4-ACETATE, 0.1 M HEPES-KOH PH REMARK 280 7.4, AND 45% 2-METHYL-2,4-PENTANEDIOL (V/V), VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 41.76000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.33850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 41.76000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 46.33850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 220 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 48 OP1 REMARK 620 2 C A 90 OP1 84.4 REMARK 620 3 C A 91 OP2 82.4 79.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 221 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 48 OP2 REMARK 620 2 C A 91 OP1 90.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 222 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 49 O2 REMARK 620 2 C A 75 OP2 79.0 REMARK 620 3 PRP A 201 O2P 85.7 94.3 REMARK 620 N 1 2 DBREF 6DLR A 1 107 PDB 6DLR 6DLR 1 107 SEQRES 1 A 107 G G A A A G U G U G U C U SEQRES 2 A 107 A G G G U U C C G C G U G SEQRES 3 A 107 C U U C G G C A C G G A C SEQRES 4 A 107 U G G U C C A A G U G A C SEQRES 5 A 107 A C A G A C G C A U U C G SEQRES 6 A 107 U G C G U U A C A C C G G SEQRES 7 A 107 A G G G A U A G A A G C C SEQRES 8 A 107 C A G G C G G G U A G G U SEQRES 9 A 107 U U CCC HET CCC A 107 23 HET PRP A 201 22 HET IRI A 202 7 HET IRI A 203 7 HET IRI A 204 7 HET IRI A 205 7 HET IRI A 206 7 HET IRI A 207 7 HET IRI A 208 7 HET IRI A 209 7 HET IRI A 210 7 HET IRI A 211 7 HET IRI A 212 7 HET IRI A 213 7 HET IRI A 214 7 HET IRI A 215 7 HET IRI A 216 7 HET IRI A 217 7 HET IRI A 218 7 HET IRI A 219 7 HET MG A 220 1 HET MG A 221 1 HET MG A 222 1 HET ACT A 223 4 HET K A 224 1 HET K A 225 1 HET K A 226 1 HETNAM CCC CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE HETNAM PRP 1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE HETNAM IRI IRIDIUM HEXAMMINE ION HETNAM MG MAGNESIUM ION HETNAM ACT ACETATE ION HETNAM K POTASSIUM ION HETSYN PRP ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID; 1-O- HETSYN 2 PRP PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOSE; 1-O- HETSYN 3 PRP PYROPHOSPHONO-5-O-PHOSPHONO-D-RIBOSE; 1-O- HETSYN 4 PRP PYROPHOSPHONO-5-O-PHOSPHONO-RIBOSE FORMUL 1 CCC C9 H13 N3 O10 P2 FORMUL 2 PRP C5 H13 O14 P3 FORMUL 3 IRI 18(H18 IR N6 3+) FORMUL 21 MG 3(MG 2+) FORMUL 24 ACT C2 H3 O2 1- FORMUL 25 K 3(K 1+) FORMUL 28 HOH *6(H2 O) LINK O3' U A 106 P CCC A 107 1555 1555 1.61 LINK OP1 G A 48 MG MG A 220 1555 1555 2.19 LINK OP2 G A 48 MG MG A 221 1555 1555 2.20 LINK O2 U A 49 MG MG A 222 1555 1555 2.42 LINK OP2 C A 75 MG MG A 222 1555 1555 2.42 LINK OP1 C A 90 MG MG A 220 1555 1555 2.20 LINK OP2 C A 91 MG MG A 220 1555 1555 2.17 LINK OP1 C A 91 MG MG A 221 1555 1555 2.14 LINK O2PAPRP A 201 MG MG A 222 1555 1555 1.99 CRYST1 83.520 92.677 74.487 90.00 121.21 90.00 C 1 2 1 4 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 0.011973 0.000000 0.007255 0.00000 SCALE2 0.000000 0.010790 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015697 0.00000