PDB Short entry for 1SYZ HEADER RNA 02-APR-04 1SYZ TITLE SOLUTION STRUCTURE OF THE S. CEREVISIAE U6 INTRAMOLECULAR STEM LOOP TITLE 2 (ISL) RNA AT PH 5.7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: U6 INTRAMOLECULAR STEM-LOOP RNA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: IN VITRO T7 RNA POLYMERASE TRANSCRIPTION. THE SOURCE 4 SEQUENCE IS FROM SACCHAROMYCES CEREVISIAE. KEYWDS RNA, STEM-LOOP, GNRA-LIKE TETRATLOOP, A-C WOBBLE PAIR, INTERNAL LOOP EXPDTA SOLUTION NMR NUMMDL 14 AUTHOR N.J.REITER,H.BLAD,F.ABILDGAARD,S.E.BUTCHER REVDAT 3 02-MAR-22 1SYZ 1 REMARK REVDAT 2 24-FEB-09 1SYZ 1 VERSN REVDAT 1 09-NOV-04 1SYZ 0 JRNL AUTH N.J.REITER,H.BLAD,F.ABILDGAARD,S.E.BUTCHER JRNL TITL DYNAMICS IN THE U6 RNA INTRAMOLECULAR STEM-LOOP: A BASE JRNL TITL 2 FLIPPING CONFORMATIONAL CHANGE. JRNL REF BIOCHEMISTRY V. 43 13739 2004 JRNL REFN ISSN 0006-2960 JRNL PMID 15504036 JRNL DOI 10.1021/BI048815Y REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.BLAD,N.J.REITER,F.ABILDGAARD,S.E.BUTCHER REMARK 1 TITL DYNAMICS IN THE U6 RNA INTRAMOLECULAR STEM LOOP STRUCTURE: REMARK 1 TITL 2 II. ANALYSIS OF CONFORMATIONAL EXCHANGE AND METAL BINDING REMARK 1 TITL 3 USING 13C NMR RELAXATION REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1, XPLORNIH 2.0.6. REMARK 3 AUTHORS : BRUNGER, A. ET AL. (CNS), CLORE, G.M. ET. AL. REMARK 3 (XPLORNIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: METHOD ALLOWED FOR THE INCORPORATION OF REMARK 3 29 RESIDUAL DIPOLAR COUPLINGS INTO THE STRUCTURE REFINEMENT REMARK 3 PROCESS. REMARK 4 REMARK 4 1SYZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-APR-04. REMARK 100 THE DEPOSITION ID IS D_1000022106. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 285; 303 REMARK 210 PH : 5.7; 5.7 REMARK 210 IONIC STRENGTH : 50 MM NACL; 50 MM NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8-1.2 MM RNA, 50 MM NACL, PH REMARK 210 5.7; 0.8-1.2 MM RNA, 50 MM NACL, REMARK 210 PH 5.7 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 2.6, SPARKY 3.0 REMARK 210 METHOD USED : XPLOR-NIH 2.0.6. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 14 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: 13C, 15N ISTOPICALLY LABELLED RNA 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 O2' A A 12 H5'' U A 13 1.39 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. = 4.4 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. = 4.6 DEGREES REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 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. = -2.8 DEGREES REMARK 500 1 A A 12 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 A A 14 N7 - C8 - N9 ANGL. DEV. = 3.6 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. = -2.6 DEGREES REMARK 500 1 G A 17 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 17 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 A A 18 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G A 20 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 G A 20 C8 - N9 - C4 ANGL. DEV. = -2.6 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. = 3.8 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. = -2.6 DEGREES REMARK 500 2 G A 10 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 G A 10 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 2 A A 12 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 A A 14 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 15 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 15 C8 - N9 - C4 ANGL. DEV. = -2.4 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. = -2.6 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. = -2.5 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. = 4.6 DEGREES REMARK 500 2 G A 20 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 A A 21 N7 - C8 - N9 ANGL. DEV. = 3.8 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. = 4.6 DEGREES REMARK 500 3 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 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. = -2.8 DEGREES REMARK 500 3 A A 12 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 3 A A 14 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 A A 15 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 G A 16 N7 - C8 - N9 ANGL. DEV. = 4.5 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. = 4.6 DEGREES REMARK 500 3 G A 17 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 255 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 S. CEREVISIAE U6 INTRAMOLECULAR STEM LOOP REMARK 900 (ISL) RNA AT PH 7.0 REMARK 900 RELATED ID: 1SY4 RELATED DB: PDB REMARK 900 REFINED SOLUTION STRUCTURE OF THE S. CEREVISIAE U6 INTRAMOLECULAR REMARK 900 STEM LOOP (ISL) RNA USING RESIDUAL DIPOLAR AT PH 7.0 REMARK 900 RELATED ID: 1SY5 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE S. CEREVISIAE U6 INTRAMOLECULAR STEM LOOP REMARK 900 (ISL) RNA USING RESIDUAL DIPOLAR AT PH 6.0 REMARK 900 RELATED ID: 1NC0 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE S. CEREVISIAE U6 INTRAMOLECULAR STEM LOOP REMARK 900 (ISL) RNA CONTAINING A U80G MUTATION REMARK 900 RELATED ID: 1NZ1 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE S. CEREVISIAE U6 INTRAMOLECULAR STEM-LOOP REMARK 900 CONTAINING AN SP PHOSPHOROTHIOATE AT NUCLEOTIDE U80 DBREF 1SYZ A 1 24 PDB 1SYZ 1SYZ 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 U G A A 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