HEADER RNA 11-SEP-97 1TLR TITLE SOLUTION STRUCTURE OF TETRALOOP RECEPTOR RNA, NMR, 20 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA TETRALOOP RECEPTOR (5'-R(GGCCUAAGACUUCGGUUAUGGCC)-3'); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TLR; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS RIBONUCLEIC ACID, TETRALOOP RECEPTOR, GROUP I INTRON, GROUP II KEYWDS 2 INTRON, RNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.E.BUTCHER,T.DIECKMANN,J.FEIGON REVDAT 3 02-MAR-22 1TLR 1 REMARK REVDAT 2 24-FEB-09 1TLR 1 VERSN REVDAT 1 12-NOV-97 1TLR 0 JRNL AUTH S.E.BUTCHER,T.DIECKMANN,J.FEIGON JRNL TITL SOLUTION STRUCTURE OF A GAAA TETRALOOP RECEPTOR RNA. JRNL REF EMBO J. V. 16 7490 1997 JRNL REFN ISSN 0261-4189 JRNL PMID 9405377 JRNL DOI 10.1093/EMBOJ/16.24.7490 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE. REMARK 4 REMARK 4 1TLR COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000176725. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.0 REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY STRUCTURES REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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: 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' A A 18 O5' U A 19 1.24 REMARK 500 O2' A A 18 H6 U A 19 1.33 REMARK 500 HO2' C A 13 O4' G A 14 1.35 REMARK 500 HO2' U A 12 O5' C A 13 1.36 REMARK 500 HO2' C A 4 O4' U A 5 1.47 REMARK 500 HO2' G A 8 O4' A A 9 1.51 REMARK 500 HO2' A A 6 O4' A A 7 1.53 REMARK 500 O2' G A 14 H5' G A 15 1.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 1 A A 9 O5' A A 9 C5' 0.115 REMARK 500 1 A A 9 C5' A A 9 C4' 0.076 REMARK 500 1 A A 9 C4' A A 9 C3' -0.068 REMARK 500 2 A A 9 O5' A A 9 C5' 0.116 REMARK 500 2 A A 9 C5' A A 9 C4' 0.081 REMARK 500 2 A A 9 C4' A A 9 C3' -0.066 REMARK 500 3 A A 9 O5' A A 9 C5' 0.115 REMARK 500 3 A A 9 C5' A A 9 C4' 0.078 REMARK 500 3 A A 9 C4' A A 9 C3' -0.068 REMARK 500 4 A A 9 O5' A A 9 C5' 0.115 REMARK 500 4 A A 9 C5' A A 9 C4' 0.080 REMARK 500 4 A A 9 C4' A A 9 C3' -0.066 REMARK 500 5 A A 9 O5' A A 9 C5' 0.116 REMARK 500 5 A A 9 C5' A A 9 C4' 0.075 REMARK 500 5 A A 9 C4' A A 9 C3' -0.069 REMARK 500 6 A A 9 O5' A A 9 C5' 0.117 REMARK 500 6 A A 9 C5' A A 9 C4' 0.080 REMARK 500 6 A A 9 C4' A A 9 C3' -0.068 REMARK 500 7 A A 9 O5' A A 9 C5' 0.114 REMARK 500 7 A A 9 C5' A A 9 C4' 0.080 REMARK 500 7 A A 9 C4' A A 9 C3' -0.067 REMARK 500 8 A A 9 O5' A A 9 C5' 0.115 REMARK 500 8 A A 9 C5' A A 9 C4' 0.077 REMARK 500 8 A A 9 C4' A A 9 C3' -0.068 REMARK 500 9 A A 9 O5' A A 9 C5' 0.114 REMARK 500 9 A A 9 C5' A A 9 C4' 0.077 REMARK 500 9 A A 9 C4' A A 9 C3' -0.069 REMARK 500 10 A A 9 O5' A A 9 C5' 0.114 REMARK 500 10 A A 9 C5' A A 9 C4' 0.076 REMARK 500 10 A A 9 C4' A A 9 C3' -0.067 REMARK 500 11 A A 9 O5' A A 9 C5' 0.115 REMARK 500 11 A A 9 C5' A A 9 C4' 0.081 REMARK 500 11 A A 9 C4' A A 9 C3' -0.068 REMARK 500 12 A A 9 O5' A A 9 C5' 0.115 REMARK 500 12 A A 9 C5' A A 9 C4' 0.081 REMARK 500 12 A A 9 C4' A A 9 C3' -0.068 REMARK 500 13 A A 9 O5' A A 9 C5' 0.115 REMARK 500 13 A A 9 C5' A A 9 C4' 0.081 REMARK 500 13 A A 9 C4' A A 9 C3' -0.069 REMARK 500 14 A A 9 O5' A A 9 C5' 0.116 REMARK 500 14 A A 9 C5' A A 9 C4' 0.079 REMARK 500 14 A A 9 C4' A A 9 C3' -0.071 REMARK 500 15 A A 9 O5' A A 9 C5' 0.115 REMARK 500 15 A A 9 C5' A A 9 C4' 0.078 REMARK 500 15 A A 9 C4' A A 9 C3' -0.068 REMARK 500 16 A A 9 O5' A A 9 C5' 0.115 REMARK 500 16 A A 9 C5' A A 9 C4' 0.077 REMARK 500 16 A A 9 C4' A A 9 C3' -0.070 REMARK 500 17 A A 9 O5' A A 9 C5' 0.114 REMARK 500 17 A A 9 C5' A A 9 C4' 0.077 REMARK 500 REMARK 500 THIS ENTRY HAS 60 BOND DEVIATIONS. 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 C5 - N7 - C8 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 G A 1 N7 - C8 - N9 ANGL. DEV. = 6.9 DEGREES REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 G A 2 C5 - N7 - C8 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 G A 2 N7 - C8 - N9 ANGL. DEV. = 6.9 DEGREES REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 A A 6 C5 - N7 - C8 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 A A 6 N7 - C8 - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 1 A A 6 C8 - N9 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 A A 7 C5 - N7 - C8 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 A A 7 N7 - C8 - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 1 A A 7 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 G A 8 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 G A 8 C5 - N7 - C8 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 G A 8 N7 - C8 - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 1 G A 8 C8 - N9 - C4 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 A A 9 O5' - C5' - C4' ANGL. DEV. = 16.8 DEGREES REMARK 500 1 A A 9 P - O5' - C5' ANGL. DEV. = -23.9 DEGREES REMARK 500 1 A A 9 C4' - C3' - O3' ANGL. DEV. = 20.8 DEGREES REMARK 500 1 A A 9 C5 - N7 - C8 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 A A 9 N7 - C8 - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 1 A A 9 C8 - N9 - C4 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 G A 14 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 14 C5 - N7 - C8 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 G A 14 N7 - C8 - N9 ANGL. DEV. = 7.1 DEGREES REMARK 500 1 G A 14 C8 - N9 - C4 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 G A 15 C5 - N7 - C8 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 G A 15 N7 - C8 - N9 ANGL. DEV. = 7.0 DEGREES REMARK 500 1 G A 15 C8 - N9 - C4 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 A A 18 C3' - C2' - C1' ANGL. DEV. = 5.1 DEGREES REMARK 500 1 A A 18 C5 - N7 - C8 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 A A 18 N7 - C8 - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 1 A A 18 C8 - N9 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 G A 20 C5 - N7 - C8 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 G A 20 N7 - C8 - N9 ANGL. DEV. = 6.9 DEGREES REMARK 500 1 G A 20 C8 - N9 - C4 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 G A 21 C5 - N7 - C8 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 G A 21 N7 - C8 - N9 ANGL. DEV. = 6.8 DEGREES REMARK 500 1 G A 21 C8 - N9 - C4 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 G A 1 C5 - N7 - C8 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 7.0 DEGREES REMARK 500 2 G A 1 C8 - N9 - C4 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 G A 2 C5 - N7 - C8 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 G A 2 N7 - C8 - N9 ANGL. DEV. = 6.8 DEGREES REMARK 500 2 G A 2 C8 - N9 - C4 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 A A 6 C5 - N7 - C8 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 A A 6 N7 - C8 - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 2 A A 6 C8 - N9 - C4 ANGL. DEV. = -3.4 DEGREES REMARK 500 2 A A 7 C5 - N7 - C8 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 A A 7 N7 - C8 - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 781 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 A A 9 0.06 SIDE CHAIN REMARK 500 2 A A 9 0.06 SIDE CHAIN REMARK 500 3 G A 8 0.05 SIDE CHAIN REMARK 500 3 A A 9 0.06 SIDE CHAIN REMARK 500 4 A A 9 0.06 SIDE CHAIN REMARK 500 5 A A 9 0.06 SIDE CHAIN REMARK 500 5 C A 13 0.06 SIDE CHAIN REMARK 500 6 A A 9 0.06 SIDE CHAIN REMARK 500 7 A A 9 0.06 SIDE CHAIN REMARK 500 8 A A 9 0.06 SIDE CHAIN REMARK 500 9 A A 9 0.05 SIDE CHAIN REMARK 500 10 A A 9 0.06 SIDE CHAIN REMARK 500 11 A A 9 0.06 SIDE CHAIN REMARK 500 12 A A 9 0.06 SIDE CHAIN REMARK 500 13 A A 9 0.06 SIDE CHAIN REMARK 500 14 A A 9 0.06 SIDE CHAIN REMARK 500 15 A A 9 0.05 SIDE CHAIN REMARK 500 16 A A 9 0.06 SIDE CHAIN REMARK 500 17 A A 9 0.06 SIDE CHAIN REMARK 500 18 A A 9 0.05 SIDE CHAIN REMARK 500 18 G A 15 0.08 SIDE CHAIN REMARK 500 19 A A 9 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1TLR A 1 23 PDB 1TLR 1TLR 1 23 SEQRES 1 A 23 G G C C U A A G A C U U C SEQRES 2 A 23 G G U U A U G G 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