10 20 30 40 50 60 70 80 1NGU - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 17-DEC-02 1NGU
TITLE NMR STRUCTURE OF PUTATIVE 3'TERMINATOR FOR B. ANTHRACIS TITLE 2 PAGA GENE NONCODING STRAND
CAVEAT 1NGU CHIRALITY ERROR AT C 15 IN CHAIN A
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'- COMPND 3 D(*CP*TP*CP*TP*CP*CP*TP*TP*GP*TP*AP*TP*TP*TP*CP*TP*TP*AP*CP COMPND 4 *AP*AP*AP*AP*AP*GP*AP*G)-3'; COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: 3' UTR HAIRPIN OF PAGA GENE, NONCODING COMPND 8 STRAND
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS ON THE NONCODING SOURCE 4 STRAND OF THE 3' UTR OF THE PAGA (110) GENE OF BACILLUS SOURCE 5 ANTHRACIS.
KEYWDS B-FORM DNA HAIRPIN
EXPDTA SOLUTION NMR
NUMMDL 5
MDLTYP MINIMIZED AVERAGE
AUTHOR P.R.SHIFLETT,K.J.TAYLOR-MCCABE,R.MICHALCZYK,L.A.SILKS, AUTHOR 2 G.GUPTA
REVDAT 2 24-FEB-09 1NGU 1 VERSN REVDAT 1 10-JUN-03 1NGU 0
JRNL AUTH P.R.SHIFLETT,K.J.TAYLOR-MCCABE,R.MICHALCZYK, JRNL AUTH 2 L.A.SILKS,G.GUPTA JRNL TITL STRUCTURAL STUDIES ON THE HAIRPINS AT THE 3' JRNL TITL 2 UNTRANSLATED REGION OF AN ANTHRAX TOXIN GENE JRNL REF BIOCHEMISTRY V. 42 6078 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 12755609 JRNL DOI 10.1021/BI034128F
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 4.1 REMARK 3 AUTHORS : PEARLMAN, D.A., CASE, D.A., CALDWELL, J.W., REMARK 3 ROSS, W.S., CHEATHAM, T.E., FERGUSON, D.M., REMARK 3 SEIBEL, G.L., SINGH, U.C., WEINER, P.K., AND REMARK 3 KOLLMAN, P.A. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE IS DERIVED FROM 206 NOES REMARK 3 OF WHICH, 23 NOES INVOLVE EXCHANGEABLE PROTONS IN THE STEM, REMARK 3 131 NOES INVOLVE NON-EXCHANGEABLE PROTONS IN THE STEM, 52 NOES REMARK 3 INVOLVE NON-EXCHANGEABLE PROTONS IN THE LOOP, 46 DISTANCE REMARK 3 RESTRAINTS INVOLVE HYDROGEN BONDS, AND 44 DIHEDRAL ANGLE REMARK 3 RESTRAINTS.
REMARK 4 REMARK 4 1NGU COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-DEC-02. REMARK 100 THE RCSB ID CODE IS RCSB017855.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 150MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM 110NC DNA; 10MM PHOSPHATE REMARK 210 BUFFER PH 6.5; 150MM NACL;; REMARK 210 2MM 110NC DNA; 10MM PHOSPHATE REMARK 210 BUFFER PH 6.5; 150MM NACL; REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY, DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 98, AMBER 4.1 REMARK 210 METHOD USED : MINIMIZATION MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 5 REMARK 210 CONFORMERS, SELECTION CRITERIA : SUBMITTED CONFORMERS INCLUDE REMARK 210 MINIMIZED AVERAGE FROM REMARK 210 MOLECULAR DYNAMICS AND 4 REMARK 210 REPRESENTATIVE DIVERGING REMARK 210 STRUCTURES. REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES.
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 2 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC A 6 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 11 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DT A 12 O4' - C1' - N1 ANGL. DEV. = 3.1 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. = 2.2 DEGREES REMARK 500 1 DT A 14 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DT A 14 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DC A 15 O4' - C1' - N1 ANGL. DEV. = 8.1 DEGREES REMARK 500 1 DT A 16 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT A 16 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DA A 20 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DA A 22 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DA A 23 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG A 25 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG A 27 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DC A 5 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DC A 6 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DT A 10 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DA A 11 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DT A 12 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DT A 13 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DT A 14 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 2 DT A 14 C6 - C5 - C7 ANGL. DEV. = -5.7 DEGREES REMARK 500 2 DC A 15 O4' - C1' - N1 ANGL. DEV. = 8.7 DEGREES REMARK 500 2 DC A 15 N1 - C2 - O2 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DT A 16 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT A 17 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DA A 20 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DA A 21 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DA A 22 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DA A 23 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DG A 27 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 3 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 3 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 DC A 6 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 104 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 DC A 6 0.06 SIDE_CHAIN REMARK 500 1 DT A 14 0.09 SIDE_CHAIN REMARK 500 1 DA A 20 0.07 SIDE_CHAIN REMARK 500 2 DT A 14 0.06 SIDE_CHAIN REMARK 500 2 DT A 16 0.07 SIDE_CHAIN REMARK 500 2 DA A 20 0.07 SIDE_CHAIN REMARK 500 3 DC A 6 0.07 SIDE_CHAIN REMARK 500 3 DA A 20 0.08 SIDE_CHAIN REMARK 500 4 DT A 10 0.06 SIDE_CHAIN REMARK 500 4 DA A 11 0.07 SIDE_CHAIN REMARK 500 4 DT A 14 0.07 SIDE_CHAIN REMARK 500 4 DA A 20 0.09 SIDE_CHAIN REMARK 500 5 DA A 20 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NGO RELATED DB: PDB REMARK 900 NMR STRUCTURE OF PUTATIVE 3' TERMINATOR FOR B. ANTHRACIS REMARK 900 PAGA GENE CODING STRAND
DBREF 1NGU A 1 27 PDB 1NGU 1NGU 1 27
SEQRES 1 A 27 DC DT DC DT DC DC DT DT DG DT DA DT DT SEQRES 2 A 27 DT DC DT DT DA DC DA DA DA DA DA DG DA SEQRES 3 A 27 DG
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