HEADER DNA 30-SEP-97 1SLS TITLE IMMOBILE SLIPPED-LOOP STRUCTURE (SLS) OF DNA HOMODIMER IN TITLE 2 SOLUTION, NMR, 9 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: OLIGODEOXYRIBONUCLEOTIDE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: HOMODIMER SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DEOXYRIBONUCLEIC ACID, DNA OLIGONUCLEOTIDE, HOMODIMER, KEYWDS 2 SLIPPED-LOOP STRUCTURE, PSEUDOKNOT, UNUSUAL STRUCTURE EXPDTA SOLUTION NMR NUMMDL 9 AUTHOR N.B.ULYANOV,V.I.IVANOV,E.E.MINYAT,E.B.KHOMYAKOVA, AUTHOR 2 M.V.PETROVA,K.LESIAK,T.L.JAMES REVDAT 2 24-FEB-09 1SLS 1 VERSN REVDAT 1 08-APR-98 1SLS 0 JRNL AUTH N.B.ULYANOV,V.I.IVANOV,E.E.MINYAT,E.B.KHOMYAKOVA, JRNL AUTH 2 M.V.PETROVA,K.LESIAK,T.L.JAMES JRNL TITL A PSEUDOSQUARE KNOT STRUCTURE OF DNA IN SOLUTION. JRNL REF BIOCHEMISTRY V. 37 12715 1998 JRNL REFN ISSN 0006-2960 JRNL PMID 9737848 JRNL DOI 10.1021/BI981018D REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA REMARK 3 AUTHORS : GUNTERT,WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1SLS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY, DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, MARDIGRAS, DYANA, REMARK 210 DNAMINICARLO, AMBER4.1, CORMA REMARK 210 METHOD USED : COMPLETE RELAXATION MATRIX REMARK 210 ANALYSIS, SIMULATED ANNEALING, REMARK 210 DISTANCE-RESTRAINED REMARK 210 MINIMIZATION, DISTANCE- REMARK 210 RESTRAINED MONTE CARLO REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 9 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 9 REMARK 210 CONFORMERS, SELECTION CRITERIA : SCORING FUNCTION (WEIGHTED REMARK 210 SUM OF DISTANCE RESTRAINTS REMARK 210 VIOLATION AND CONFORMATIONAL REMARK 210 ENERGY) 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 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 DT A 3 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT A 11 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DT A 11 C6 - C5 - C7 ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DT A 12 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DT A 12 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DT A 13 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DT A 13 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DT A 14 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DT A 14 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DT A 15 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DG A 16 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT A 17 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DG A 18 N1 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DG A 22 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DG A 24 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT B 28 C6 - C5 - C7 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DC B 30 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DT B 36 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DT B 36 C6 - C5 - C7 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DT B 37 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DT B 38 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DT B 38 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DT B 39 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DT B 39 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DT B 40 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT B 40 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DG B 41 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT B 42 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DG B 49 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DT A 3 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DT A 11 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DT A 11 C4 - C5 - C7 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DT A 11 C6 - C5 - C7 ANGL. DEV. = -6.7 DEGREES REMARK 500 2 DT A 12 C4' - C3' - C2' ANGL. DEV. = -4.6 DEGREES REMARK 500 2 DT A 12 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 DT A 12 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 2 DT A 13 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DT A 13 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DT A 14 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DT A 15 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT A 17 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DT B 28 C6 - C5 - C7 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 DC B 30 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DT B 36 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DT B 36 C6 - C5 - C7 ANGL. DEV. = -6.2 DEGREES REMARK 500 2 DT B 37 C4' - C3' - C2' ANGL. DEV. = -4.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 275 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 DT A 11 0.08 SIDE_CHAIN REMARK 500 1 DC B 27 0.06 SIDE_CHAIN REMARK 500 1 DT B 36 0.09 SIDE_CHAIN REMARK 500 1 DG B 47 0.09 SIDE_CHAIN REMARK 500 2 DC A 2 0.06 SIDE_CHAIN REMARK 500 2 DT A 8 0.06 SIDE_CHAIN REMARK 500 2 DG A 10 0.06 SIDE_CHAIN REMARK 500 2 DC B 27 0.07 SIDE_CHAIN REMARK 500 2 DC B 29 0.06 SIDE_CHAIN REMARK 500 2 DT B 33 0.06 SIDE_CHAIN REMARK 500 2 DG B 35 0.06 SIDE_CHAIN REMARK 500 2 DG B 47 0.09 SIDE_CHAIN REMARK 500 3 DC A 4 0.07 SIDE_CHAIN REMARK 500 3 DG A 10 0.08 SIDE_CHAIN REMARK 500 3 DT A 11 0.07 SIDE_CHAIN REMARK 500 3 DT A 12 0.09 SIDE_CHAIN REMARK 500 3 DC B 27 0.06 SIDE_CHAIN REMARK 500 3 DC B 29 0.09 SIDE_CHAIN REMARK 500 3 DT B 37 0.08 SIDE_CHAIN REMARK 500 3 DG B 47 0.07 SIDE_CHAIN REMARK 500 4 DG A 10 0.10 SIDE_CHAIN REMARK 500 4 DG B 35 0.07 SIDE_CHAIN REMARK 500 4 DG B 47 0.10 SIDE_CHAIN REMARK 500 5 DC A 4 0.08 SIDE_CHAIN REMARK 500 5 DT A 11 0.10 SIDE_CHAIN REMARK 500 5 DT A 14 0.08 SIDE_CHAIN REMARK 500 5 DC B 27 0.07 SIDE_CHAIN REMARK 500 5 DC B 29 0.10 SIDE_CHAIN REMARK 500 5 DT B 36 0.09 SIDE_CHAIN REMARK 500 5 DT B 39 0.07 SIDE_CHAIN REMARK 500 5 DG B 47 0.06 SIDE_CHAIN REMARK 500 6 DT A 15 0.07 SIDE_CHAIN REMARK 500 6 DG B 35 0.08 SIDE_CHAIN REMARK 500 6 DT B 36 0.11 SIDE_CHAIN REMARK 500 6 DG B 47 0.09 SIDE_CHAIN REMARK 500 7 DC A 2 0.06 SIDE_CHAIN REMARK 500 7 DC A 4 0.11 SIDE_CHAIN REMARK 500 7 DC A 6 0.06 SIDE_CHAIN REMARK 500 7 DT A 8 0.06 SIDE_CHAIN REMARK 500 7 DG A 10 0.07 SIDE_CHAIN REMARK 500 7 DT A 11 0.07 SIDE_CHAIN REMARK 500 7 DC B 27 0.07 SIDE_CHAIN REMARK 500 7 DT B 33 0.06 SIDE_CHAIN REMARK 500 7 DG B 35 0.09 SIDE_CHAIN REMARK 500 8 DG A 10 0.11 SIDE_CHAIN REMARK 500 8 DG A 22 0.06 SIDE_CHAIN REMARK 500 8 DC B 27 0.06 SIDE_CHAIN REMARK 500 8 DC B 29 0.07 SIDE_CHAIN REMARK 500 8 DT B 39 0.06 SIDE_CHAIN REMARK 500 8 DG B 47 0.10 SIDE_CHAIN REMARK 500 9 DC A 5 0.12 SIDE_CHAIN REMARK 500 9 DG A 10 0.13 SIDE_CHAIN REMARK 500 9 DG B 35 0.07 SIDE_CHAIN REMARK 500 9 DG B 47 0.08 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1SLS A 1 25 PDB 1SLS 1SLS 1 25 DBREF 1SLS B 26 50 PDB 1SLS 1SLS 26 50 SEQRES 1 A 25 DG DC DT DC DC DC DA DT DG DG DT DT DT SEQRES 2 A 25 DT DT DG DT DG DC DA DC DG DA DG DC SEQRES 1 B 25 DG DC DT DC DC DC DA DT DG DG DT DT DT SEQRES 2 B 25 DT DT DG DT DG DC DA DC DG DA DG DC 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 191 0 0 0 0 0 0 6 0 0 0 4 END