HEADER RNA 14-NOV-13 4NLF TITLE 2'-TRIFLUOROMETHYLTHIO-2'-DEOXYCYTIDINE-MODIFIED SRL COMPND MOL_ID: 1; COMPND 2 MOLECULE: 23S RIBOSOMAL RNA SARCIN RICIN LOOP; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS RNA HAIRPIN, STRUCTURAL, RNA EXPDTA X-RAY DIFFRACTION AUTHOR E.ENNIFAR,R.MICURA,M.KOSUTIC REVDAT 3 20-SEP-23 4NLF 1 REMARK REVDAT 2 15-JUN-22 4NLF 1 JRNL REMARK LINK REVDAT 1 19-NOV-14 4NLF 0 JRNL AUTH M.KOSUTIC,L.JUD,C.DA VEIGA,M.FRENER,K.FAUSTER,C.KREUTZ, JRNL AUTH 2 E.ENNIFAR,R.MICURA JRNL TITL SURPRISING BASE PAIRING AND STRUCTURAL PROPERTIES OF JRNL TITL 2 2'-TRIFLUOROMETHYLTHIO-MODIFIED RIBONUCLEIC ACIDS. JRNL REF J.AM.CHEM.SOC. V. 136 6656 2014 JRNL REFN ESSN 1520-5126 JRNL PMID 24766131 JRNL DOI 10.1021/JA5005637 REMARK 2 REMARK 2 RESOLUTION. 1.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.040 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 35121 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.099 REMARK 3 R VALUE (WORKING SET) : 0.099 REMARK 3 FREE R VALUE : 0.116 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.430 REMARK 3 FREE R VALUE TEST SET COUNT : 1204 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 29.1786 - 2.0799 0.99 3980 141 0.1290 0.1556 REMARK 3 2 2.0799 - 1.6509 0.98 3876 135 0.1012 0.1117 REMARK 3 3 1.6509 - 1.4422 0.97 3836 134 0.0872 0.1016 REMARK 3 4 1.4422 - 1.3104 0.96 3788 135 0.0846 0.1093 REMARK 3 5 1.3104 - 1.2164 0.95 3770 131 0.0754 0.0863 REMARK 3 6 1.2164 - 1.1447 0.95 3711 139 0.0744 0.0887 REMARK 3 7 1.1447 - 1.0874 0.94 3709 126 0.0741 0.0947 REMARK 3 8 1.0874 - 1.0400 0.93 3642 138 0.0729 0.0938 REMARK 3 9 1.0400 - 1.0000 0.92 3605 125 0.0799 0.0935 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.50 REMARK 3 SHRINKAGE RADIUS : 0.40 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.030 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 8.530 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 : 0.008 671 REMARK 3 ANGLE : 1.523 1051 REMARK 3 CHIRALITY : 0.065 138 REMARK 3 PLANARITY : 0.028 28 REMARK 3 DIHEDRAL : 13.763 332 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 4NLF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1000083350. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAR-13 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 : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.708 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69037 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.03100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 38.7800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.09300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 15.80 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: PDB ENTRY 3DVZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1:1 RNA (IN 1.0 MM SODIUM EDTA, PH REMARK 280 8.0, 10 MM TRIS, PH 8.0) TO WELL SOLUTION (3.1 M AMMONIUM REMARK 280 SULFATE, 50 MM POTASSIUM MOPS, 10 MM MAGNESIUM CHLORIDE, 10 MM REMARK 280 MANGANESE CHLORIDE), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K, PH 7.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 19.78500 REMARK 290 SMTRY3 2 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: 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 OP2 A A 2654 O HOH A 2850 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 G A2671 O5' - P - OP1 ANGL. DEV. = 9.1 DEGREES REMARK 500 G A2671 O5' - P - OP2 ANGL. DEV. = -9.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 G A2659 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2701 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DVZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E.COLI 23S RRNA REMARK 900 RELATED ID: 1Q9A RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E.COLI 23S RRNA REMARK 900 RELATED ID: 3DW4 RELATED DB: PDB REMARK 900 RELATED ID: 3DW5 RELATED DB: PDB REMARK 900 RELATED ID: 3DW6 RELATED DB: PDB REMARK 900 RELATED ID: 3DW7 RELATED DB: PDB REMARK 900 RELATED ID: 4NMG RELATED DB: PDB REMARK 900 2'TRIFLUOROMETHYLTHIO-2'-DEOXYURIDINE-MODIFIED SRL REMARK 900 RELATED ID: 4NXH RELATED DB: PDB DBREF 4NLF A 2647 2673 PDB 4NLF 4NLF 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 6FC G G A G U SEQRES 3 A 27 G HET 6FC A2667 34 HET SO4 A2701 5 HETNAM 6FC 2'-TRIFLUOROMETHYLTHIO-2'-DEOXYCYTIDINE HETNAM SO4 SULFATE ION FORMUL 1 6FC C10 H15 F3 N3 O7 P S FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *183(H2 O) LINK O3' C A2666 P 6FC A2667 1555 1555 1.60 LINK O3' 6FC A2667 P G A2668 1555 1555 1.61 SITE 1 AC1 5 C A2651 C A2652 HOH A2823 HOH A2844 SITE 2 AC1 5 HOH A2875 CRYST1 29.170 39.570 29.920 90.00 90.92 90.00 P 1 21 1 2 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 0.034282 0.000000 0.000552 0.00000 SCALE2 0.000000 0.025272 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033427 0.00000