10 20 30 40 50 60 70 80 1NP5 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 17-JAN-03 1NP5
TITLE (GAC)3 PARALLEL DUPLEX
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*AP*CP*GP*AP*CP*GP*AP*C)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE IS FOUND IN TRIPLET REPEAT SOURCE 4 EXPANSION INVOLVING NEUROGENETIC DISEASES.
KEYWDS DNA TRINUCLEOTIDE REPEAT, PARALLEL DUPLEX, HOMO-BASEPAIR KEYWDS 2 MISMATCH, NMR SOLUTION STRUCTURE
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR M.ZHENG,X.HAN,X.GAO
REVDAT 2 24-FEB-09 1NP5 1 VERSN REVDAT 1 11-FEB-03 1NP5 0
JRNL AUTH M.ZHENG,X.HAN,X.GAO JRNL TITL STRAND POLARITY OF TRINUCLEOTIDE REPEAT SEQUENCES: JRNL TITL 2 NMR STUDIES OF PARALLEL/ANTI-PARARELL JRNL TITL 3 DUPLEX,{D(GAC)3}2 JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : MARDIGRAS 3.0 REMARK 3 AUTHORS : BORGIAS, B.A. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1NP5 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JAN-03. REMARK 100 THE RCSB ID CODE IS RCSB018071.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 273 REMARK 210 PH : 4.7 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2 MM 5'-D(GACGACGAC), 0.1 M REMARK 210 NACL, 10 MM SODIUM PHOSPHATE, REMARK 210 0.1 MM EDTA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY, DQF-COSY, REMARK 210 COSY-35, 1H-31P COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : UXNMR 940101, FELIX 95, X- REMARK 210 PLOR 3.01 REMARK 210 METHOD USED : DISTANCE GEOMETRY, RESTRAINT REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS 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 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG A 1 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 DA A 2 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 DA A 2 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG A 4 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 DG A 4 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA A 5 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG A 7 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 DG A 7 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DA A 8 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG B 101 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG B 101 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG B 101 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 DA B 102 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 DA B 102 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 DC B 103 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG B 104 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG B 104 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG B 104 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DA B 105 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA B 105 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG B 107 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG B 107 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 DG B 107 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DA B 108 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC B 109 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES 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 DA A 2 0.07 SIDE_CHAIN REMARK 500 DA A 5 0.06 SIDE_CHAIN REMARK 500 DA B 102 0.07 SIDE_CHAIN REMARK 500 DA B 105 0.06 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
DBREF 1NP5 A 1 9 PDB 1NP5 1NP5 1 9 DBREF 1NP5 B 101 109 PDB 1NP5 1NP5 101 109
SEQRES 1 A 9 DG DA DC DG DA DC DG DA DC SEQRES 1 B 9 DG DA DC DG DA DC DG DA 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