HEADER RNA 02-JUN-18 6DLQ TITLE PRPP RIBOSWITCH BOUND TO PRPP, MANGANESE CHLORIDE 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 KEYWDS RIBOSWITCH, NON-CODING, RNA, YKKC EXPDTA X-RAY DIFFRACTION AUTHOR A.PESELIS,A.SERGANOV REVDAT 4 13-MAR-24 6DLQ 1 HETSYN REVDAT 3 29-JUL-20 6DLQ 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 01-JAN-20 6DLQ 1 REMARK REVDAT 1 14-NOV-18 6DLQ 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. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC (1.12_2829: ???) REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 21504 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.170 REMARK 3 FREE R VALUE TEST SET COUNT : 2188 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 19.9838 - 6.9556 0.96 1235 134 0.1777 0.2181 REMARK 3 2 6.9556 - 5.5601 0.98 1281 137 0.1894 0.2228 REMARK 3 3 5.5601 - 4.8688 0.98 1230 154 0.1726 0.1990 REMARK 3 4 4.8688 - 4.4290 0.98 1287 136 0.2030 0.2120 REMARK 3 5 4.4290 - 4.1145 0.98 1228 145 0.2033 0.2288 REMARK 3 6 4.1145 - 3.8738 0.99 1250 145 0.2130 0.2299 REMARK 3 7 3.8738 - 3.6810 0.99 1264 138 0.2267 0.2512 REMARK 3 8 3.6810 - 3.5217 0.98 1285 135 0.2506 0.3293 REMARK 3 9 3.5217 - 3.3868 0.98 1257 139 0.2583 0.2909 REMARK 3 10 3.3868 - 3.2704 0.96 1194 165 0.2571 0.2451 REMARK 3 11 3.2704 - 3.1686 0.96 1271 116 0.2887 0.3455 REMARK 3 12 3.1686 - 3.0783 0.93 1143 159 0.3189 0.3392 REMARK 3 13 3.0783 - 2.9976 0.93 1239 122 0.3522 0.3454 REMARK 3 14 2.9976 - 2.9247 0.89 1134 118 0.3904 0.3870 REMARK 3 15 2.9247 - 2.8584 0.86 1084 143 0.4536 0.4206 REMARK 3 16 2.8584 - 2.7977 0.73 934 102 0.5863 0.6085 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) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.580 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 2606 REMARK 3 ANGLE : 0.580 4070 REMARK 3 CHIRALITY : 0.026 537 REMARK 3 PLANARITY : 0.003 108 REMARK 3 DIHEDRAL : 16.224 1298 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 6DLQ 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_1000234879. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-SEP-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 : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21504 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 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 (%) : 98.4 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 20.00 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.51800 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 (%): 64.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.43 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 291.15K 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 42.66050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.25300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 42.66050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 45.25300 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 MN A 213 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GTP A 1 O2G REMARK 620 2 G A 103 OP2 133.6 REMARK 620 3 G A 103 N7 76.1 126.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 205 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 14 OP2 REMARK 620 2 G A 15 N7 86.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 218 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 30 OP1 REMARK 620 2 G A 31 O6 95.0 REMARK 620 3 U A 84 O3' 131.0 76.5 REMARK 620 4 U A 84 O2' 127.1 73.1 4.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 202 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 48 OP1 REMARK 620 2 C A 90 OP1 71.4 REMARK 620 3 C A 91 OP2 78.5 80.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 203 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 48 OP2 REMARK 620 2 C A 91 OP1 80.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 211 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 48 O6 REMARK 620 2 PRP A 201 O1P 71.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 207 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 49 O2 REMARK 620 2 C A 75 OP2 85.9 REMARK 620 3 PRP A 201 O2P 85.1 92.4 REMARK 620 N 1 2 DBREF 6DLQ A 1 107 PDB 6DLQ 6DLQ 1 107 SEQRES 1 A 107 GTP 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 GTP A 1 32 HET CCC A 107 23 HET PRP A 201 22 HET MN A 202 1 HET MN A 203 1 HET MN A 204 1 HET MN A 205 1 HET MN A 206 1 HET MN A 207 1 HET MN A 208 1 HET MN A 209 1 HET MN A 210 1 HET MN A 211 1 HET MN A 212 1 HET MN A 213 1 HET NA A 214 1 HET NA A 215 1 HET NA A 216 1 HET NA A 217 1 HET K A 218 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM CCC CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE HETNAM PRP 1-O-PYROPHOSPHONO-5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM 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 GTP C10 H16 N5 O14 P3 FORMUL 1 CCC C9 H13 N3 O10 P2 FORMUL 2 PRP C5 H13 O14 P3 FORMUL 3 MN 12(MN 2+) FORMUL 15 NA 4(NA 1+) FORMUL 19 K K 1+ FORMUL 20 HOH *8(H2 O) LINK O3' GTP A 1 P G A 2 1555 1555 1.60 LINK O3' U A 106 P CCC A 107 1555 1555 1.61 LINK O2G GTP A 1 MN MN A 213 1555 1555 2.29 LINK OP2 A A 14 MN MN A 205 1555 1555 2.62 LINK N7 G A 15 MN MN A 205 1555 1555 2.57 LINK O4 U A 18 MN MN A 210 1555 1555 2.65 LINK OP1 C A 30 K K A 218 1555 1555 2.94 LINK O6 G A 31 K K A 218 1555 1555 3.38 LINK N7 A A 38 MN MN A 209 1555 1555 2.76 LINK OP1 G A 48 MN MN A 202 1555 1555 2.39 LINK OP2 G A 48 MN MN A 203 1555 1555 2.28 LINK O6 G A 48 MN MN A 211 1555 1555 2.52 LINK O2 U A 49 MN MN A 207 1555 1555 2.18 LINK OP2 C A 75 MN MN A 207 1555 1555 2.03 LINK O3' U A 84 K K A 218 1555 2555 3.19 LINK O2' U A 84 K K A 218 1555 2555 3.02 LINK OP1 C A 90 MN MN A 202 1555 1555 2.31 LINK OP2 C A 91 MN MN A 202 1555 1555 2.17 LINK OP1 C A 91 MN MN A 203 1555 1555 2.28 LINK OP1 G A 94 MN MN A 204 1555 1555 2.35 LINK OP2 G A 103 MN MN A 213 1555 1555 2.52 LINK N7 G A 103 MN MN A 213 1555 1555 2.49 LINK O2PAPRP A 201 MN MN A 207 1555 1555 2.05 LINK O1PAPRP A 201 MN MN A 211 1555 1555 2.48 CRYST1 85.321 90.506 73.482 90.00 122.52 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 0.011720 0.000000 0.007472 0.00000 SCALE2 0.000000 0.011049 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016139 0.00000 HETATM 1 PG GTP A 1 -2.460 50.512 57.469 1.00152.37 P HETATM 2 O1G GTP A 1 -1.379 50.968 56.517 1.00132.77 O HETATM 3 O2G GTP A 1 -3.482 49.699 56.710 1.00139.63 O HETATM 4 O3G GTP A 1 -1.861 49.673 58.572 1.00146.79 O HETATM 5 O3B GTP A 1 -3.202 51.802 58.088 1.00149.59 O HETATM 6 PB GTP A 1 -3.904 51.791 59.541 1.00163.07 P HETATM 7 O1B GTP A 1 -5.017 52.811 59.615 1.00152.26 O HETATM 8 O2B GTP A 1 -4.432 50.407 59.834 1.00162.03 O HETATM 9 O3A GTP A 1 -2.721 52.137 60.583 1.00157.05 O HETATM 10 PA GTP A 1 -1.387 52.921 60.126 1.00147.58 P HETATM 11 O1A GTP A 1 -0.423 51.980 59.443 1.00133.94 O HETATM 12 O2A GTP A 1 -0.732 53.583 61.315 1.00118.69 O HETATM 13 O5' GTP A 1 -1.906 54.029 59.079 1.00144.45 O HETATM 14 C5' GTP A 1 -1.860 55.402 59.390 1.00135.47 C HETATM 15 C4' GTP A 1 -3.021 55.774 60.301 1.00128.64 C HETATM 16 O4' GTP A 1 -2.611 55.628 61.639 1.00108.26 O HETATM 17 C3' GTP A 1 -3.391 57.240 60.173 1.00124.48 C HETATM 18 O3' GTP A 1 -4.404 57.454 59.218 1.00129.34 O HETATM 19 C2' GTP A 1 -3.836 57.665 61.562 1.00117.45 C HETATM 20 O2' GTP A 1 -5.132 57.178 61.831 1.00125.25 O HETATM 21 C1' GTP A 1 -2.807 56.844 62.331 1.00115.96 C HETATM 22 N9 GTP A 1 -1.508 57.550 62.319 1.00124.18 N HETATM 23 C8 GTP A 1 -0.290 56.926 62.240 1.00118.07 C HETATM 24 N7 GTP A 1 0.686 57.859 62.253 1.00112.40 N HETATM 25 C5 GTP A 1 0.113 59.078 62.344 1.00123.15 C HETATM 26 C6 GTP A 1 0.660 60.354 62.394 1.00130.86 C HETATM 27 O6 GTP A 1 1.879 60.507 62.353 1.00139.01 O HETATM 28 N1 GTP A 1 -0.168 61.453 62.489 1.00124.28 N HETATM 29 C2 GTP A 1 -1.536 61.272 62.533 1.00120.03 C HETATM 30 N2 GTP A 1 -2.350 62.321 62.626 1.00111.69 N HETATM 31 N3 GTP A 1 -2.068 59.999 62.484 1.00121.90 N HETATM 32 C4 GTP A 1 -1.266 58.907 62.388 1.00125.58 C