HEADER RNA 22-NOV-16 5WQ1 TITLE SOLUTION STRUCTURE OF THE FIRST STEM-LOOP OF ESCHERICHIA COLI DSRA RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DSRA-SL1; 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 FIRST STEM-LOOP, RNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR P.WU,J.WU,Y.SHI REVDAT 3 14-JUN-23 5WQ1 1 REMARK REVDAT 2 01-NOV-17 5WQ1 1 JRNL REVDAT 1 05-JUL-17 5WQ1 0 JRNL AUTH P.WU,X.LIU,L.YANG,Y.SUN,Q.GONG,J.WU,Y.SHI JRNL TITL THE IMPORTANT CONFORMATIONAL PLASTICITY OF DSRA SRNA FOR JRNL TITL 2 ADAPTING MULTIPLE TARGET REGULATION JRNL REF NUCLEIC ACIDS RES. V. 45 9625 2017 JRNL REFN ESSN 1362-4962 JRNL PMID 28934467 JRNL DOI 10.1093/NAR/GKX570 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5WQ1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1300002182. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283; 303 REMARK 210 PH : 6.5; 6.5 REMARK 210 IONIC STRENGTH : 60; 60 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 0.7 MM RNA (23-MER), 10 MM REMARK 210 SODIUM PHOSPHATE, 50 MM SODIUM REMARK 210 CHLORIDE, 90% H2O/10% D2O; 0.7 REMARK 210 MM RNA (23-MER), 10 MM SODIUM REMARK 210 PHOSPHATE, 50 MM SODIUM CHLORIDE, REMARK 210 100% D2O; 0.7 MM [U-13C; U-15N] REMARK 210 RNA (23-MER), 10 MM SODIUM REMARK 210 PHOSPHATE, 50 MM POTASSIUM REMARK 210 CHLORIDE, 90% H2O/10% D2O; 0.7 REMARK 210 MM [U-13C; U-15N] RNA (23-MER), REMARK 210 10 MM SODIUM PHOSPHATE, 50 MM REMARK 210 SODIUM CHLORIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-15N HNN REMARK 210 -COSY; 2D 1H-15N HSQC; 2D 1H-15N REMARK 210 HSQC NH2 ONLY; 3D 1H-15N NOESY; REMARK 210 2D DQF-COSY; 2D 1H-1H TOCSY; 2D REMARK 210 1H-13C HSQC ALIPHATIC; 2D 1H-13C REMARK 210 HSQC AROMATIC; 2D HCN; 3D HCCH- REMARK 210 TOCSY; 3D HCCH-COSY; 3D 1H-13C REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : DMX; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, XWINNMR, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 160 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 1 A A 3 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 A A 3 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 A A 3 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 C A 4 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 A A 5 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 5 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A A 5 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 C A 7 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 A A 8 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 8 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A A 8 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 A A 10 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A A 10 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 C A 14 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 C A 15 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 C A 22 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 C A 23 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 A A 3 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 A A 3 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 C A 4 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 A A 5 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 A A 5 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 A A 5 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 C A 7 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 A A 8 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 A A 8 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 A A 10 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 10 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 C A 14 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 C A 15 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 C A 22 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 C A 23 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 3 A A 3 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 3 A A 3 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 3 C A 4 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 3 A A 5 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 3 A A 5 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 3 A A 5 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 3 C A 7 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 3 A A 8 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 A A 8 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 3 A A 10 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 3 A A 10 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 A A 10 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 3 C A 14 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 3 C A 15 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 3 C A 22 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 3 C A 23 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 4 A A 3 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 A A 3 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 340 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 26934 RELATED DB: BMRB DBREF 5WQ1 A 1 23 PDB 5WQ1 5WQ1 1 23 SEQRES 1 A 23 G G A C A U C A G A U U U SEQRES 2 A 23 C C U G G U G U C C CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1