HEADER DNA-RNA HYBRID 25-JUL-20 7JJF TITLE SARCIN-RICIN LOOP WITH MODIFIED RESIDUE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA/DNA (27-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 4 ORGANISM_TAXID: 562 KEYWDS SARCIN-RICIN LOOP, RNA CRYSTAL STRUCTURE, RNA TETRALOOPS, RNA, DNA- KEYWDS 2 RNA HYBRID EXPDTA X-RAY DIFFRACTION AUTHOR J.M.HARP,P.S.PALLAN,M.EGLI REVDAT 2 18-OCT-23 7JJF 1 REMARK REVDAT 1 23-DEC-20 7JJF 0 JRNL AUTH P.S.PALLAN,T.P.LYBRAND,M.K.SCHLEGEL,J.M.HARP,H.JAHNS, JRNL AUTH 2 M.MANOHARAN,M.EGLI JRNL TITL INCORPORATING A THIOPHOSPHATE MODIFICATION INTO A COMMON RNA JRNL TITL 2 TETRALOOP MOTIF CAUSES AN UNANTICIPATED STABILITY BOOST. JRNL REF BIOCHEMISTRY V. 59 4627 2020 JRNL REFN ISSN 0006-2960 JRNL PMID 33275419 JRNL DOI 10.1021/ACS.BIOCHEM.0C00685 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 4.580 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 36363 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.650 REMARK 3 FREE R VALUE TEST SET COUNT : 3874 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 29.3400 - 3.2600 0.90 1770 190 0.1383 0.1873 REMARK 3 2 3.2500 - 2.5900 0.90 1794 203 0.1376 0.1842 REMARK 3 3 2.5800 - 2.2600 0.90 1740 198 0.1455 0.1570 REMARK 3 4 2.2600 - 2.0500 0.90 1800 203 0.1476 0.1699 REMARK 3 5 2.0500 - 1.9000 0.90 1789 194 0.1541 0.2058 REMARK 3 6 1.9000 - 1.7900 0.90 1764 206 0.1432 0.1807 REMARK 3 7 1.7900 - 1.7000 0.90 1766 198 0.1521 0.1723 REMARK 3 8 1.7000 - 1.6300 0.89 1742 204 0.1494 0.1685 REMARK 3 9 1.6300 - 1.5700 0.90 1792 204 0.1553 0.1904 REMARK 3 10 1.5700 - 1.5100 0.89 1762 190 0.1846 0.2215 REMARK 3 11 1.5100 - 1.4600 0.88 1737 187 0.2038 0.2376 REMARK 3 12 1.4600 - 1.4200 0.87 1705 191 0.2266 0.2868 REMARK 3 13 1.4200 - 1.3900 0.84 1645 195 0.2536 0.2474 REMARK 3 14 1.3900 - 1.3500 0.80 1590 187 0.2753 0.2796 REMARK 3 15 1.3500 - 1.3200 0.73 1445 173 0.2914 0.3119 REMARK 3 16 1.3200 - 1.2900 0.74 1476 164 0.3134 0.3704 REMARK 3 17 1.2900 - 1.2700 0.73 1405 155 0.2999 0.3113 REMARK 3 18 1.2700 - 1.2400 0.67 1361 152 0.3116 0.3984 REMARK 3 19 1.2400 - 1.2200 0.67 1262 147 0.3341 0.3446 REMARK 3 20 1.2200 - 1.2000 0.64 1320 157 0.3445 0.3783 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 41.508 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 4.79 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.76 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 : 0.007 675 REMARK 3 ANGLE : 1.342 1049 REMARK 3 CHIRALITY : 0.054 140 REMARK 3 PLANARITY : 0.009 28 REMARK 3 DIHEDRAL : 15.367 351 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 7JJF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1000250842. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAR-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) : N REMARK 200 RADIATION SOURCE : LIQUID ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : EXCILLUM METALJET D2+ 70 KV REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.3418 REMARK 200 MONOCHROMATOR : MULTI-LAYER CONFOCAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : BRUKER PHOTON III REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROTEUM PLUS REMARK 200 DATA SCALING SOFTWARE : PROTEUM PLUS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 27.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 17.00 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.4700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24 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: PHASER REMARK 200 STARTING MODEL: 3DVZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RNA WAS DISSOLVED IN 1 MM NA2 EDTA (PH REMARK 280 8.0) AND 10 MM TRIS-HCL (PH 8.0) TO ATTAIN 350 UM FINAL RNA REMARK 280 CONCENTRATION. THE RNA SAMPLE WAS ANNEALED BY HEATING AT 65 C REMARK 280 FOR 2 MIN AND SLOWLY COOLING TO ROOM TEMPERATURE. REMARK 280 CRYSTALLIZATION SET-UPS WERE MADE BY MIXING 4 UL OF RNA SOLUTION REMARK 280 WITH 2 UL OF A CRYSTALLIZATION BUFFER COMPOSED OF 3.0 M AMMONIUM REMARK 280 SULFATE, 10 MM MAGNESIUM CHLORIDE, 10 MM MANGANESE CHLORIDE, AND REMARK 280 50 MM POTASSIUM 3-(N-MORPHOLINO) PROPANESULFONIC ACID (MOPS), PH REMARK 280 7.0 AT 18 C. CRYSTALS APPEAR IN ABOUT TWO WEEKS TIME., VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 37.83050 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 56.74575 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 18.91525 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 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 C A 52 C6 - N1 - C2 ANGL. DEV. = 2.5 DEGREES REMARK 500 G A 59 C4 - C5 - N7 ANGL. DEV. = -3.3 DEGREES REMARK 500 G A 59 C5 - N7 - C8 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA A 60 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES REMARK 500 VC7 A 74 O3' - P - OP1 ANGL. DEV. = 13.8 DEGREES REMARK 500 A A 75 O3' - P - OP1 ANGL. DEV. = 8.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 7JJF A 47 86 PDB 7JJF 7JJF 47 86 SEQRES 1 A 27 U G C U C C U A G U A C G SEQRES 2 A 27 DA VC7 A G G A C C G G A G U SEQRES 3 A 27 G HET VC7 A 74 37 HET MG A 101 1 HETNAM VC7 5'-O-[(R)-HYDROXY(METHYL)PHOSPHORYL]GUANOSINE HETNAM MG MAGNESIUM ION FORMUL 1 VC7 C11 H16 N5 O7 P FORMUL 2 MG MG 2+ FORMUL 3 HOH *103(H2 O) LINK O3' DA A 60 P VC7 A 74 1555 1555 1.56 LINK O3' VC7 A 74 P A A 75 1555 1555 1.60 LINK O2' VC7 A 74 MG MG A 101 1555 1555 2.72 CRYST1 29.340 29.340 75.661 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 0.034083 0.000000 0.000000 0.00000 SCALE2 0.000000 0.034083 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013217 0.00000