10 20 30 40 50 60 70 80 135D - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 30-AUG-93 135D
TITLE SOLUTION STRUCTURE OF A PURINE(DOT)PURINE(DOT)PYRIMIDINE TITLE 2 DNA TRIPLEX CONTAINING G(DOT)GC AND T(DOT)AT TRIPLES
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA TRIPLEX; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED
KEYWDS DNA, NMR, TRIPLEX
EXPDTA SOLUTION NMR
AUTHOR I.RADHAKRISHNAN,D.J.PATEL
REVDAT 3 24-FEB-09 135D 1 VERSN REVDAT 2 01-APR-03 135D 1 JRNL REVDAT 1 30-APR-94 135D 0
JRNL AUTH I.RADHAKRISHNAN,D.J.PATEL JRNL TITL SOLUTION STRUCTURE OF A PURINE.PURINE.PYRIMIDINE JRNL TITL 2 DNA TRIPLEX CONTAINING G.GC AND T.AT TRIPLES. JRNL REF STRUCTURE V. 1 135 1993 JRNL REFN ISSN 0969-2126 JRNL PMID 8069626 JRNL DOI 10.1016/0969-2126(93)90028-F
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH I.RADHAKRISHNAN,D.J.PATEL REMARK 1 TITL SOLUTION STRUCTURE OF AN INTRAMOLECULAR REMARK 1 TITL 2 PURINE(DOT)PURINE(DOT)PYRIMIDINE DNA TRIPLEX REMARK 1 REF J.AM.CHEM.SOC. V. 115 1615 1993 REMARK 1 REFN ISSN 0002-7863
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESTRAINED MOLECULAR DYNAMICS REMARK 3 CALCULATIONS WERE DONE ONIDEALIZED A'- AND B-FORM STARTING REMARK 3 STRUCTURES. ONLY THE TRIPLEX REGION AND THE FIRST AND LAST REMARK 3 RESIDUES OF EACH OF THE TWO LOOPS IN THE SEQUENCE WERE REMARK 3 CONSIDERED. THE REFINEMENT WAS CONDUCTED IN TWO STAGES. IN THE REMARK 3 FIRST STAGE, SIX STRUCTURES WERE CALCULATED (THREE FROM EACH REMARK 3 STARTING STRUCTURE) USING DISTANCE RESTRAINTS. IN THE SECOND REMARK 3 STAGE, TWO OF THE SIX STRUCTURES WERE REFINED DIRECTLY AGAINST REMARK 3 PRIMARY NOE DATA. THE R(1/6) VALUE WAS USED TO MONITOR THE REMARK 3 REFINEMENT DURING THIS STAGE. THE FINAL R(1/6) VALUES FOR THE REMARK 3 TWO AVERAGED MINIMIZED STRUCTURES WERE 0.04 AND 0.045.
REMARK 4 REMARK 4 135D 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) : 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 : RESTRAINED MOLECULAR REMARK 210 DYNAMICS, DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 RES C SSSEQI REMARK 465 DT A 2L REMARK 465 DT A 3L REMARK 465 DT A 4L REMARK 465 DT A 7L REMARK 465 DT A 8L REMARK 465 DT A 9L
REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 RES CSSEQI ATOMS REMARK 470 DT A 5L P OP1 OP2 REMARK 470 DT A 10L P OP1 OP2
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 DT A 1 C3' DT A 1 C2' 0.078 REMARK 500 DT A 1 C2' DT A 1 C1' 0.063 REMARK 500 DT A 1 C5 DT A 1 C7 0.038 REMARK 500 DC A 2 N1 DC A 2 C6 0.040 REMARK 500 DC A 3 N1 DC A 3 C6 0.037 REMARK 500 DT A 4 C5 DT A 4 C7 0.042 REMARK 500 DC A 5 N1 DC A 5 C6 0.047 REMARK 500 DT A 7 C5 DT A 7 C7 0.050 REMARK 500 DT A 5L C5 DT A 5L C7 0.042 REMARK 500 DA A 8 C2' DA A 8 C1' 0.065 REMARK 500 DG A 9 C4' DG A 9 C3' 0.117 REMARK 500 DG A 9 C3' DG A 9 C2' 0.124 REMARK 500 DG A 9 C2' DG A 9 C1' 0.063 REMARK 500 DA A 11 C4' DA A 11 C3' 0.061 REMARK 500 DA A 11 C3' DA A 11 C2' 0.100 REMARK 500 DT A 6L C3' DT A 6L C2' 0.082 REMARK 500 DT A 6L C2' DT A 6L C1' 0.102 REMARK 500 DT A 15 C3' DT A 15 C2' 0.123 REMARK 500 DT A 15 C2' DT A 15 C1' 0.063 REMARK 500 DG A 17 C2' DG A 17 C1' 0.083 REMARK 500 DT A 18 C3' DT A 18 C2' 0.128 REMARK 500 DT A 18 C2' DT A 18 C1' 0.111 REMARK 500 DT A 18 C5 DT A 18 C7 0.043 REMARK 500 DG A 19 C2' DG A 19 C1' 0.085 REMARK 500 DG A 20 C3' DG A 20 C2' 0.077 REMARK 500 DG A 20 C2' DG A 20 C1' 0.098 REMARK 500 DT A 21 C4' DT A 21 C3' 0.080 REMARK 500 DT A 21 C5 DT A 21 C7 0.041 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 DT A 1 O4' - C1' - C2' ANGL. DEV. = -5.9 DEGREES REMARK 500 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC A 2 C4' - C3' - C2' ANGL. DEV. = -4.2 DEGREES REMARK 500 DC A 2 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 DC A 2 N1 - C2 - O2 ANGL. DEV. = 4.3 DEGREES REMARK 500 DC A 2 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = -7.1 DEGREES REMARK 500 DT A 4 C1' - O4' - C4' ANGL. DEV. = -7.6 DEGREES REMARK 500 DT A 4 O4' - C1' - C2' ANGL. DEV. = -6.9 DEGREES REMARK 500 DT A 4 O4' - C1' - N1 ANGL. DEV. = 8.5 DEGREES REMARK 500 DT A 4 N3 - C2 - O2 ANGL. DEV. = -3.8 DEGREES REMARK 500 DC A 5 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT A 7 C1' - O4' - C4' ANGL. DEV. = -7.1 DEGREES REMARK 500 DT A 7 O4' - C1' - C2' ANGL. DEV. = -6.4 DEGREES REMARK 500 DT A 7 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT A 1L C6 - C5 - C7 ANGL. DEV. = -4.8 DEGREES REMARK 500 DT A 5L C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG A 10 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA A 11 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG A 13 O4' - C1' - C2' ANGL. DEV. = -8.8 DEGREES REMARK 500 DG A 13 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 DA A 14 O4' - C1' - N9 ANGL. DEV. = 6.9 DEGREES REMARK 500 DT A 6L O4' - C1' - N1 ANGL. DEV. = -8.7 DEGREES REMARK 500 DT A 6L C4 - C5 - C6 ANGL. DEV. = 4.1 DEGREES REMARK 500 DT A 6L C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 DT A 10L C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 DT A 10L O4' - C1' - C2' ANGL. DEV. = -5.7 DEGREES REMARK 500 DT A 10L O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT A 15 C1' - O4' - C4' ANGL. DEV. = -8.4 DEGREES REMARK 500 DT A 15 C4' - C3' - C2' ANGL. DEV. = -8.5 DEGREES REMARK 500 DT A 15 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 DT A 15 N1 - C2 - N3 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT A 15 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 DG A 16 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 DG A 17 C1' - O4' - C4' ANGL. DEV. = 4.4 DEGREES REMARK 500 DT A 18 C4' - C3' - C2' ANGL. DEV. = -4.5 DEGREES REMARK 500 DT A 18 N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES REMARK 500 DT A 18 C6 - C5 - C7 ANGL. DEV. = -5.8 DEGREES REMARK 500 DG A 20 C1' - O4' - C4' ANGL. DEV. = 5.6 DEGREES REMARK 500 DG A 20 O3' - P - O5' ANGL. DEV. = -11.6 DEGREES REMARK 500 DT A 21 O4' - C4' - C3' ANGL. DEV. = -3.5 DEGREES REMARK 500 DT A 21 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 DT A 21 C4' - C3' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 DT A 21 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 134D RELATED DB: PDB REMARK 900 MINIMIZED AVERAGE STRUCTURE REMARK 900 RELATED ID: 136D RELATED DB: PDB REMARK 900 ENSEMBLE OF 14 STRUCTURES
DBREF 135D A 1 21 PDB 135D 135D 1 21
SEQRES 1 A 31 DT DC DC DT DC DC DT DT DT DT DT DT DA SEQRES 2 A 31 DG DG DA DG DG DA DT DT DT DT DT DT DG SEQRES 3 A 31 DG DT DG DG DT
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