HEADER RNA 31-JUL-20 6ZYB TITLE SARCIN-RICIN LOOP RNA FROM ECOLI WITH A C2667-2'-OCF3 MODIFICATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SARCIN-RICIN LOOP RNA FROM ECOLI WITH A C2667-2'-OCF3 COMPND 3 MODIFICATION; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS RIBOSOME, MODIFICATION, RNA EXPDTA X-RAY DIFFRACTION AUTHOR E.ENNIFAR REVDAT 3 31-JAN-24 6ZYB 1 REMARK REVDAT 2 23-JUN-21 6ZYB 1 JRNL REVDAT 1 16-DEC-20 6ZYB 0 JRNL AUTH M.HIMMELSTOSS,K.ERHARTER,E.RENARD,E.ENNIFAR,C.KREUTZ, JRNL AUTH 2 R.MICURA JRNL TITL 2'- O -TRIFLUOROMETHYLATED RNA - A POWERFUL MODIFICATION FOR JRNL TITL 2 RNA CHEMISTRY AND NMR SPECTROSCOPY. JRNL REF CHEM SCI V. 11 11322 2020 JRNL REFN ISSN 2041-6520 JRNL PMID 34094374 JRNL DOI 10.1039/D0SC04520A REMARK 2 REMARK 2 RESOLUTION. 0.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.090 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 96381 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.132 REMARK 3 R VALUE (WORKING SET) : 0.131 REMARK 3 FREE R VALUE : 0.149 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 4824 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 29.5000 - 2.8000 1.00 3056 163 0.1106 0.1321 REMARK 3 2 2.8000 - 2.2200 1.00 3053 162 0.1294 0.1593 REMARK 3 3 2.2200 - 1.9400 1.00 3043 160 0.1317 0.1526 REMARK 3 4 1.9400 - 1.7600 1.00 3074 164 0.1146 0.1048 REMARK 3 5 1.7600 - 1.6400 1.00 3027 158 0.1073 0.1200 REMARK 3 6 1.6400 - 1.5400 1.00 3053 159 0.1151 0.1295 REMARK 3 7 1.5400 - 1.4600 1.00 3063 163 0.1261 0.1440 REMARK 3 8 1.4600 - 1.4000 1.00 3010 159 0.1310 0.1477 REMARK 3 9 1.4000 - 1.3400 1.00 3059 162 0.1296 0.1713 REMARK 3 10 1.3400 - 1.3000 1.00 3083 163 0.1353 0.1453 REMARK 3 11 1.3000 - 1.2600 1.00 3086 163 0.1323 0.1347 REMARK 3 12 1.2600 - 1.2200 1.00 2998 156 0.1310 0.1528 REMARK 3 13 1.2200 - 1.1900 1.00 3078 162 0.1293 0.1398 REMARK 3 14 1.1900 - 1.1600 1.00 3072 161 0.1365 0.1651 REMARK 3 15 1.1600 - 1.1300 1.00 3011 159 0.1416 0.1579 REMARK 3 16 1.1300 - 1.1100 1.00 3094 162 0.1397 0.1676 REMARK 3 17 1.1100 - 1.0900 1.00 3056 160 0.1521 0.1875 REMARK 3 18 1.0900 - 1.0700 1.00 3013 159 0.1542 0.1624 REMARK 3 19 1.0700 - 1.0500 1.00 3060 160 0.1613 0.1729 REMARK 3 20 1.0500 - 1.0300 1.00 3054 161 0.1775 0.1817 REMARK 3 21 1.0300 - 1.0100 1.00 3036 161 0.1936 0.2413 REMARK 3 22 1.0100 - 1.0000 1.00 3066 162 0.1892 0.1955 REMARK 3 23 1.0000 - 0.9800 1.00 3007 156 0.2449 0.3041 REMARK 3 24 0.9800 - 0.9700 1.00 3128 165 0.2536 0.2714 REMARK 3 25 0.9700 - 0.9600 1.00 3037 161 0.2568 0.3163 REMARK 3 26 0.9600 - 0.9400 1.00 3048 160 0.2783 0.2879 REMARK 3 27 0.9400 - 0.9300 1.00 3059 161 0.2914 0.2672 REMARK 3 28 0.9300 - 0.9200 1.00 3014 159 0.3192 0.3108 REMARK 3 29 0.9200 - 0.9100 1.00 3110 165 0.3482 0.3653 REMARK 3 30 0.9100 - 0.9000 1.00 3009 158 0.3765 0.3911 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.30 REMARK 3 SHRINKAGE RADIUS : 0.00 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.131 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.221 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.49 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 : 0.007 741 REMARK 3 ANGLE : 1.552 1156 REMARK 3 CHIRALITY : 0.055 151 REMARK 3 PLANARITY : 0.026 32 REMARK 3 DIHEDRAL : 11.672 361 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 6ZYB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1292110478. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 96381 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.900 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 39.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 45.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.92 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: 3DVZ REMARK 200 REMARK 200 REMARK: PLATELET REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.2 M AMMONIUM SULFATE, 50 MM REMARK 280 POTASSIUM MOPS, PH 7.0, 10 MM MAGNESIUM CHLORIDE, 10 MM REMARK 280 MANGANESE CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 38.56500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 57.84750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.28250 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 H1 G A 2648 O2 U A 2672 1.45 REMARK 500 H21 G A 2648 O HOH A 2701 1.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2845 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH A2846 DISTANCE = 6.67 ANGSTROMS DBREF 6ZYB A 2647 2673 PDB 6ZYB 6ZYB 2647 2673 SEQRES 1 A 27 U G C U C C U A G U A C G SEQRES 2 A 27 A G A G G A C QSK G G A G U SEQRES 3 A 27 G HET QSK A2667 33 HETNAM QSK [(2~{R},3~{R},4~{R},5~{R})-5-(4-AZANYL-2-OXIDANYLIDENE- HETNAM 2 QSK PYRIMIDIN-1-YL)-3-OXIDANYL-4-(TRIFLUOROMETHYLOXY) HETNAM 3 QSK OXOLAN-2-YL]METHOXYPHOSPHINIC ACID FORMUL 1 QSK C10 H13 F3 N3 O7 P FORMUL 2 HOH *146(H2 O) LINK O3' C A2666 P QSK A2667 1555 1555 1.61 LINK O3' QSK A2667 P G A2668 1555 1555 1.62 CRYST1 29.500 29.500 77.130 90.00 90.00 90.00 P 43 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 0.033898 0.000000 0.000000 0.00000 SCALE2 0.000000 0.033898 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012965 0.00000