HEADER RNA 07-OCT-01 1K4A TITLE STRUCTURE OF AGAA RNA TETRALOOP, NMR, 20 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*GP*UP*UP*CP*AP*GP*AP*AP*GP*AP*AP*CP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: AN RNA HAIRPIN WITH AGAA TETRALOOP, THE PRIMARY COMPND 6 RECOGNITION SITE FOR S. CEREVISIAE RNASE III. SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS RIBONUCLEIC ACID, TETRALOOP, RNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.WU,P.K.YANG,S.E.BUTCHER,S.KANG,G.CHANFREAU,J.FEIGON REVDAT 4 22-MAY-24 1K4A 1 REMARK REVDAT 3 23-FEB-22 1K4A 1 REMARK REVDAT 2 24-FEB-09 1K4A 1 VERSN REVDAT 1 19-DEC-01 1K4A 0 JRNL AUTH H.WU,P.K.YANG,S.E.BUTCHER,S.KANG,G.CHANFREAU,J.FEIGON JRNL TITL A NOVEL FAMILY OF RNA TETRALOOP STRUCTURE FORMS THE JRNL TITL 2 RECOGNITION SITE FOR SACCHAROMYCES CEREVISIAE RNASE III. JRNL REF EMBO J. V. 20 7240 2001 JRNL REFN ISSN 0261-4189 JRNL PMID 11743000 JRNL DOI 10.1093/EMBOJ/20.24.7240 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: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 326 RESTRAINTS, 300 ARE NOE-DERIVED DISTANCE RESTRAINTS, 54 REMARK 3 DIHEDRAL ANGLE RESTRAINTS. ADDITIONAL 26 DISTANCE RESTRAINTS REMARK 3 FROM HYDROGEN BONDS ARE USED IN THE STEM REGION. REMARK 4 REMARK 4 1K4A COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-OCT-01. REMARK 100 THE DEPOSITION ID IS D_1000014542. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 274; 293 REMARK 210 PH : 6.3; 6.3 REMARK 210 IONIC STRENGTH : 10MM; 10MM REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 2MM RNA HAIRPIN, 10MM NACL, PH REMARK 210 6.3, 90% H2O, 10% D2O; 2MM RNA REMARK 210 HAIRPIN, 10MM NACL, PH 6.3, 90% REMARK 210 H2O, 10% D2O; 1MM 13C/15N REMARK 210 LABELED RNA HAIRPIN, 10MM NACL, REMARK 210 PH 6.3, 99.99% D2O; 1MM 13C/15N REMARK 210 LABELED RNA HAIRPIN,10MM NACL, REMARK 210 PH 6.3, 99.99% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_13C-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX; AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2000 REMARK 210 METHOD USED : DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 6 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 G A 7 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G A 7 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 8 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 9 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G A 10 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 10 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 11 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 12 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 A A 6 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 G A 7 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 7 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 A A 8 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 A A 9 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 10 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 10 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A A 11 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 12 N7 - C8 - N9 ANGL. DEV. = 3.8 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. = 4.4 DEGREES REMARK 500 3 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 3 A A 6 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 G A 7 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 G A 7 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 A A 8 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 A A 9 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 G A 10 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 10 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 3 A A 11 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 A A 12 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 4 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 4 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 4 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 4 A A 6 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 G A 7 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 4 G A 7 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 4 A A 8 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 4 A A 9 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 G A 10 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 G A 10 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 274 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1K4B RELATED DB: PDB REMARK 900 STRUCTURE OF AGUU RNA TETRALOOP, NMR, 20 STRUCTURES DBREF 1K4A A 1 14 PDB 1K4A 1K4A 1 14 SEQRES 1 A 14 G G U U C A G A A G A A C SEQRES 2 A 14 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