HEADER RNA 14-FEB-03 1NZ1 TITLE SOLUTION STRUCTURE OF THE S. CEREVISIAE U6 INTRAMOLECULAR STEM-LOOP TITLE 2 CONTAINING AN SP PHOSPHOROTHIOATE AT NUCLEOTIDE U80 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SP U6 INTRAMOLECULAR STEM-LOOP RNA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SP ISL RNA; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: A62G, SP PHOSHPHOROTHIOATE MODIFIED U80 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHETIC RNA (DHARMACON, INC.) WAS PREPARED SOURCE 4 CONTAINING AN SP PHOSPHOROTHIOATE MODIFICATION AT NUCLEOTIDE U80. SOURCE 5 THE SP RNA WAS SEPARATED FROM THE RP RNA DIASTEREOMER USING REVERSE- SOURCE 6 PHASE HIGH PRESSURE LIQUID CHROMATOGRAPHY. KEYWDS U6 RNA, STEM-LOOP, PHOSPHOROTHIOATE, SP PHOSPHOROTHIOATE, RESIDUAL KEYWDS 2 DIPOLAR COUPLING, RDC, RNA EXPDTA SOLUTION NMR NUMMDL 17 AUTHOR N.J.REITER,L.J.NIKSTAD,A.M.ALLMAN,R.J.JOHNSON,S.E.BUTCHER REVDAT 3 23-FEB-22 1NZ1 1 REMARK LINK REVDAT 2 24-FEB-09 1NZ1 1 VERSN REVDAT 1 13-MAY-03 1NZ1 0 JRNL AUTH N.J.REITER,L.J.NIKSTAD,A.M.ALLMAN,R.J.JOHNSON,S.E.BUTCHER JRNL TITL STRUCTURE OF THE U6 RNA INTRAMOLECULAR STEM-LOOP HARBORING JRNL TITL 2 AN S(P)-PHOSPHOROTHIOATE MODIFICATION. JRNL REF RNA V. 9 533 2003 JRNL REFN ISSN 1355-8382 JRNL PMID 12702812 JRNL DOI 10.1261/RNA.2199103 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, X-PLOR 3.1 REMARK 3 AUTHORS : BRUKER (XWINNMR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NZ1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1000018370. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283; 303; 303 REMARK 210 PH : 7.0; 7.2; 7.0 REMARK 210 IONIC STRENGTH : 50 MM NACL; 50 MM NACL; 50 MM REMARK 210 NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8-1.2 MM RNA, 50 MM NACL, PH REMARK 210 7.0; 0.8-1.2 MM RNA, 50 MM NACL, REMARK 210 PH 7.0, 17 MG/ML PF1 PHAGE; 0.8- REMARK 210 1.2 MM RNA, 50 MM NACL, PH 7.0 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; HSQC; 2D TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ; 500 MHZ; 400 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 98, SPARKY 3, CNS 1.1 REMARK 210 METHOD USED : TORSION ANGLE AND MOLECULAR REMARK 210 DYNAMICS, SIMULATED ANNEALING, REMARK 210 RESIDUAL DIPOLAR COUPLING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 17 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 15 REMARK 210 REMARK 210 REMARK: SOLUTION STRUCTURE BASED ON 322 NOE DERIVED DISTANCE REMARK 210 RESTRAINTS, 144 DIHEDRAL ANGLE RESTRAINTS, 25 HYDROGEN BOND REMARK 210 RESTRAINTS, AND 40 RESIDUAL DIPOLAR COPUPLING RESTRAINTS. 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: CLOSE CONTACTS 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 HO2' C A 11 O4' A A 12 1.53 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 1 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 G A 10 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 10 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 12 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 14 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 15 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G A 16 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 16 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 17 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G A 17 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 18 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 G A 20 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 20 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 21 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 22 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 10 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 10 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A A 12 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 14 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 15 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 16 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 16 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 17 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 17 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 A A 18 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 G A 20 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 G A 20 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 2 A A 21 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 22 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 3 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 G A 10 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 G A 10 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 3 A A 12 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 A A 14 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 A A 15 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 G A 16 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 G A 16 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 G A 17 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 17 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 A A 18 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 310 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LC6 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE U6 INTRAMOLECULAR STEM-LOOP RNA REMARK 900 RELATED ID: 1NYZ RELATED DB: PDB REMARK 900 REFINED SOLUTION STRUCTURE OF THE U6 INTRAMOLECULAR STEM-LOOP RNA REMARK 900 USING RESIDUAL DIPOLAR COUPLINGS (RDCS) REMARK 900 RELATED ID: 1NC0 RELATED DB: PDB REMARK 900 U80G U6 INTRAMOLECULAR STEM-LOOP RNA FROM SACCHAROMYCES CEREVISIAE REMARK 900 RELATED ID: 5703 RELATED DB: BMRB DBREF 1NZ1 A 1 24 PDB 1NZ1 1NZ1 1 24 SEQRES 1 A 24 G G U U C C C C U G C A U SEQRES 2 A 24 A A G G A SSU G A A C C MODRES 1NZ1 SSU A 19 U URIDINE-5'-PHOSPHOROTHIOATE HET SSU A 19 30 HETNAM SSU URIDINE-5'-PHOSPHOROTHIOATE HETSYN SSU SP-SULFUR-SUBSTITUTED URIDINE FORMUL 1 SSU C9 H13 N2 O8 P S LINK O3' A A 18 P SSU A 19 1555 1555 1.61 LINK O3' SSU A 19 P G A 20 1555 1555 1.61 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