HEADER RNA 17-FEB-12 2LPT TITLE MOLECULAR DYNAMICS RE-REFINEMENT OF DOMAIN 5 OF THE PYLAIELLA TITLE 2 LITTORALIS GROUP II INTRON COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA_(34-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS RNA, TETRALOOP, BULGE EXPDTA SOLUTION NMR NUMMDL 5 AUTHOR N.M.HENRIKSEN,D.R.DAVIS,T.E.CHEATHAM III REVDAT 2 01-MAY-24 2LPT 1 REMARK REVDAT 1 08-AUG-12 2LPT 0 JRNL AUTH N.M.HENRIKSEN,D.R.DAVIS,T.E.CHEATHAM III JRNL TITL MOLECULAR DYNAMICS RE-REFINEMENT OF TWO DIFFERENT SMALL RNA JRNL TITL 2 LOOP STRUCTURES USING THE ORIGINAL NMR DATA SUGGEST A COMMON JRNL TITL 3 STRUCTURE. JRNL REF J.BIOMOL.NMR V. 53 321 2012 JRNL REFN ISSN 0925-2738 JRNL PMID 22714631 JRNL DOI 10.1007/S10858-012-9642-5 REMARK 0 REMARK 0 THIS ENTRY 2LPT REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL REMARK 0 STRUCTURAL DATA (2F88.MR) DETERMINED BY AUTHORS OF THE PDB ENTRY REMARK 0 2F88: M.SEETHARAMAN,N.V.ELDHO,R.A.PADGETT,K.T.DAYIE REMARK 0 ORIGINAL DATA REFERENCE 1 REMARK 0 PDB ID: 2F88 REMARK 0 AUTH M.SEETHARAMAN,N.V.ELDHO,R.A.PADGETT,K.T.DAYIE REMARK 0 TITL STRUCTURE OF A SELF-SPLICING GROUP II INTRON CATALYTIC REMARK 0 TITL 2 EFFECTOR DOMAIN 5: PARALLELS WITH SPLICEOSOMAL U6 RNA. REMARK 0 REF RNA V. 12 235 2006 REMARK 0 REFN ISSN 1355-8382 REMARK 0 PMID 16428604 REMARK 0 DOI 10.1261/RNA.2237806 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 11 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 2LPT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000102681. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL 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 : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 5 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 5 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: AUTHOR USED THE MR DATA FROM ENTRY 2F88. 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 2 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 2 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 C A 4 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 C A 5 O4' - C1' - N1 ANGL. DEV. = 6.6 DEGREES REMARK 500 1 C A 5 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 G A 8 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 1 C A 11 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 A A 13 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 13 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A A 13 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 A A 16 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 16 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 A A 17 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 A A 17 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 17 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 A A 18 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 A A 18 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 C A 21 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 C A 23 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 A A 24 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 A A 24 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 24 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 A A 25 N9 - C1' - C2' ANGL. DEV. = -6.6 DEGREES REMARK 500 1 A A 25 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 A A 25 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 A A 25 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 C A 27 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 A A 28 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A A 28 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 C A 29 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 U A 32 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 C A 34 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 A A 2 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 A A 2 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 A A 2 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 C A 4 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 C A 5 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 2 C A 5 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 G A 8 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 U A 9 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 C A 11 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 A A 13 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 A A 13 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 A A 13 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 2 A A 16 C3' - C2' - C1' ANGL. DEV. = 5.5 DEGREES REMARK 500 2 A A 16 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 16 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 2 A A 17 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 A A 17 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 2 A A 18 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 179 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 G A 3 0.07 SIDE CHAIN REMARK 500 1 G A 6 0.09 SIDE CHAIN REMARK 500 1 G A 15 0.11 SIDE CHAIN REMARK 500 1 A A 17 0.06 SIDE CHAIN REMARK 500 1 C A 21 0.07 SIDE CHAIN REMARK 500 1 G A 22 0.09 SIDE CHAIN REMARK 500 1 A A 24 0.13 SIDE CHAIN REMARK 500 1 A A 28 0.06 SIDE CHAIN REMARK 500 1 U A 33 0.09 SIDE CHAIN REMARK 500 2 G A 3 0.07 SIDE CHAIN REMARK 500 2 G A 6 0.08 SIDE CHAIN REMARK 500 2 G A 15 0.10 SIDE CHAIN REMARK 500 2 A A 16 0.05 SIDE CHAIN REMARK 500 2 G A 22 0.08 SIDE CHAIN REMARK 500 2 A A 24 0.12 SIDE CHAIN REMARK 500 2 U A 33 0.07 SIDE CHAIN REMARK 500 3 G A 3 0.06 SIDE CHAIN REMARK 500 3 C A 4 0.06 SIDE CHAIN REMARK 500 3 G A 6 0.07 SIDE CHAIN REMARK 500 3 A A 13 0.07 SIDE CHAIN REMARK 500 3 G A 15 0.10 SIDE CHAIN REMARK 500 3 G A 22 0.07 SIDE CHAIN REMARK 500 3 A A 24 0.12 SIDE CHAIN REMARK 500 3 A A 28 0.06 SIDE CHAIN REMARK 500 4 G A 3 0.08 SIDE CHAIN REMARK 500 4 C A 4 0.07 SIDE CHAIN REMARK 500 4 G A 6 0.07 SIDE CHAIN REMARK 500 4 G A 10 0.06 SIDE CHAIN REMARK 500 4 G A 15 0.11 SIDE CHAIN REMARK 500 4 A A 16 0.08 SIDE CHAIN REMARK 500 4 A A 24 0.12 SIDE CHAIN REMARK 500 4 A A 25 0.09 SIDE CHAIN REMARK 500 4 C A 27 0.08 SIDE CHAIN REMARK 500 4 A A 28 0.06 SIDE CHAIN REMARK 500 4 U A 33 0.07 SIDE CHAIN REMARK 500 5 G A 3 0.07 SIDE CHAIN REMARK 500 5 C A 4 0.08 SIDE CHAIN REMARK 500 5 G A 6 0.07 SIDE CHAIN REMARK 500 5 G A 15 0.09 SIDE CHAIN REMARK 500 5 A A 17 0.06 SIDE CHAIN REMARK 500 5 A A 24 0.08 SIDE CHAIN REMARK 500 5 G A 26 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2F88 RELATED DB: PDB REMARK 900 NMR STRUCTURE OF DOMAIN 5 OF GROUP II INTRON. THIS ENTRY 2LPT REMARK 900 REFLECTS AN ALTERNATIVE MODELING OF NMR DATA 2F88.MR REMARK 900 RELATED ID: 2LPS RELATED DB: PDB REMARK 900 RELATED ID: 18275 RELATED DB: BMRB DBREF 2LPT A 1 34 PDB 2LPT 2LPT 1 34 SEQRES 1 A 34 G A G C C G U G U G C G A SEQRES 2 A 34 U G A A A G U C G C A A G SEQRES 3 A 34 C A C G G U U 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