HEADER RNA 02-JUN-18 6DLS TITLE PRPP RIBOSWITCH BOUND TO PRPP, THALLIUM ACETATE 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 27-APR-22 6DLS 1 SPRSDE HETSYN REVDAT 3 29-JUL-20 6DLS 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 01-JAN-20 6DLS 1 SPRSDE REVDAT 1 14-NOV-18 6DLS 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. 2.89 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) : 2.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 3 NUMBER OF REFLECTIONS : 19937 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1974 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 19.3503 - 6.8556 0.91 1276 144 0.1587 0.1570 REMARK 3 2 6.8556 - 5.4822 0.94 1330 129 0.1801 0.2206 REMARK 3 3 5.4822 - 4.8013 0.93 1264 146 0.1781 0.1814 REMARK 3 4 4.8013 - 4.3678 0.94 1320 138 0.2032 0.2534 REMARK 3 5 4.3678 - 4.0579 0.96 1341 129 0.2035 0.2516 REMARK 3 6 4.0579 - 3.8205 0.96 1317 160 0.2148 0.2285 REMARK 3 7 3.8205 - 3.6305 0.97 1363 141 0.2254 0.2420 REMARK 3 8 3.6305 - 3.4734 0.98 1353 159 0.2282 0.3069 REMARK 3 9 3.4734 - 3.3404 0.96 1304 151 0.2342 0.3008 REMARK 3 10 3.3404 - 3.2257 0.96 1314 151 0.2571 0.3658 REMARK 3 11 3.2257 - 3.1253 0.93 1275 141 0.3120 0.3712 REMARK 3 12 3.1253 - 3.0363 0.90 1245 167 0.3490 0.3957 REMARK 3 13 3.0363 - 2.9566 0.87 1197 115 0.3857 0.4470 REMARK 3 14 2.9566 - 2.8847 0.76 1064 103 0.4312 0.4409 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) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.810 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 : 0.010 2606 REMARK 3 ANGLE : 1.400 4070 REMARK 3 CHIRALITY : 0.055 537 REMARK 3 PLANARITY : 0.008 108 REMARK 3 DIHEDRAL : 19.460 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 6DLS 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_1000234882. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-OCT-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) : 0.9795 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 : 19937 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.885 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 (%) : 97.9 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 19.35 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.82600 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 (%): 65.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.54 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 42.61000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.98850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 42.61000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 45.98850 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 U A 63 O3' C A 64 P -0.091 REMARK 500 G A 94 O3' G A 95 P -0.079 REMARK 500 G A 95 O3' C A 96 P -0.074 REMARK 500 C A 96 O3' G A 97 P -0.091 REMARK 500 G A 97 O3' G A 98 P -0.092 REMARK 500 REMARK 500 REMARK: NULL 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 TL A 202 TL REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 30 OP1 REMARK 620 2 G A 31 N7 89.1 REMARK 620 3 U A 84 O3' 129.5 63.6 REMARK 620 4 U A 84 O2' 125.6 60.3 4.3 REMARK 620 5 A A 85 OP1 130.9 66.8 3.2 7.1 REMARK 620 6 A A 85 N7 124.4 56.2 7.6 4.1 10.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 48 OP1 REMARK 620 2 C A 90 OP1 89.2 REMARK 620 3 C A 91 OP2 89.4 79.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 204 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 48 OP2 REMARK 620 2 C A 91 OP1 66.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 205 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 49 O2 REMARK 620 2 C A 75 OP2 79.5 REMARK 620 3 PRP A 201 O2P 71.5 99.4 REMARK 620 N 1 2 DBREF 6DLS A 1 107 PDB 6DLS 6DLS 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 TL A 202 1 HET MG A 203 1 HET MG A 204 1 HET MG A 205 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 TL THALLIUM (I) ION HETNAM MG MAGNESIUM 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 TL TL 1+ FORMUL 4 MG 3(MG 2+) FORMUL 7 HOH *(H2 O) LINK O3' GTP A 1 P G A 2 1555 1555 1.61 LINK O3' U A 106 P CCC A 107 1555 1555 1.61 LINK OP1 C A 30 TL TL A 202 1555 2555 2.91 LINK N7 G A 31 TL TL A 202 1555 2555 2.54 LINK OP1 G A 48 MG MG A 203 1555 1555 2.13 LINK OP2 G A 48 MG MG A 204 1555 1555 2.60 LINK O2 U A 49 MG MG A 205 1555 1555 2.31 LINK OP2 C A 75 MG MG A 205 1555 1555 2.09 LINK O3' U A 84 TL TL A 202 1555 1555 2.79 LINK O2' U A 84 TL TL A 202 1555 1555 3.29 LINK OP1 A A 85 TL TL A 202 1555 1555 3.17 LINK N7 A A 85 TL TL A 202 1555 1555 3.25 LINK OP1 C A 90 MG MG A 203 1555 1555 2.24 LINK OP2 C A 91 MG MG A 203 1555 1555 2.01 LINK OP1 C A 91 MG MG A 204 1555 1555 2.34 LINK O2PAPRP A 201 MG MG A 205 1555 1555 2.08 CRYST1 85.220 91.977 75.058 90.00 122.80 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 0.011734 0.000000 0.007562 0.00000 SCALE2 0.000000 0.010872 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015850 0.00000 HETATM 1 PG GTP A 1 -4.542 50.588 60.958 1.00158.24 P HETATM 2 O1G GTP A 1 -4.902 49.369 60.138 1.00151.99 O HETATM 3 O2G GTP A 1 -3.036 50.779 60.911 1.00149.25 O HETATM 4 O3G GTP A 1 -5.002 50.408 62.389 1.00149.88 O HETATM 5 O3B GTP A 1 -5.308 51.844 60.286 1.00146.92 O HETATM 6 PB GTP A 1 -5.177 53.333 60.897 1.00146.81 P HETATM 7 O1B GTP A 1 -5.776 54.357 59.956 1.00134.72 O HETATM 8 O2B GTP A 1 -5.808 53.424 62.272 1.00142.83 O HETATM 9 O3A GTP A 1 -3.570 53.503 60.957 1.00141.25 O HETATM 10 PA GTP A 1 -2.701 53.769 62.289 1.00142.20 P HETATM 11 O1A GTP A 1 -1.389 53.018 62.164 1.00130.45 O HETATM 12 O2A GTP A 1 -3.410 53.406 63.577 1.00138.67 O HETATM 13 O5' GTP A 1 -2.493 55.364 62.140 1.00130.41 O HETATM 14 C5' GTP A 1 -3.246 56.097 61.184 1.00119.86 C HETATM 15 C4' GTP A 1 -4.396 56.869 61.830 1.00117.45 C HETATM 16 O4' GTP A 1 -4.089 57.021 63.189 1.00115.31 O HETATM 17 C3' GTP A 1 -4.507 58.303 61.317 1.00113.35 C HETATM 18 O3' GTP A 1 -5.480 58.486 60.323 1.00113.19 O HETATM 19 C2' GTP A 1 -4.906 59.153 62.502 1.00108.21 C HETATM 20 O2' GTP A 1 -6.282 58.985 62.738 1.00115.15 O HETATM 21 C1' GTP A 1 -4.079 58.396 63.530 1.00110.52 C HETATM 22 N9 GTP A 1 -2.716 58.950 63.383 1.00104.21 N HETATM 23 C8 GTP A 1 -1.559 58.264 63.091 1.00104.42 C HETATM 24 N7 GTP A 1 -0.537 59.142 63.032 1.00101.29 N HETATM 25 C5 GTP A 1 -1.026 60.380 63.285 1.00103.67 C HETATM 26 C6 GTP A 1 -0.419 61.631 63.358 1.00104.36 C HETATM 27 O6 GTP A 1 0.782 61.707 63.163 1.00 96.59 O HETATM 28 N1 GTP A 1 -1.155 62.771 63.644 1.00105.65 N HETATM 29 C2 GTP A 1 -2.520 62.645 63.860 1.00111.90 C HETATM 30 N2 GTP A 1 -3.261 63.722 64.136 1.00116.55 N HETATM 31 N3 GTP A 1 -3.120 61.394 63.788 1.00110.06 N HETATM 32 C4 GTP A 1 -2.390 60.277 63.506 1.00103.94 C