10 20 30 40 50 60 70 80 1BE5 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 19-MAY-98 1BE5
TITLE STRUCTURAL STUDIES OF A STABLE PARALLEL-STRANDED DNA DUPLEX TITLE 2 INCORPORATING ISOGUANINE:CYTOSINE AND ISOCYTOSINE:GUANINE TITLE 3 BASE PAIRS BY NMR, MINIMIZED AVERAGE STRUCTURE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA DUPLEX (TGCACGGACT); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA DUPLEX (TGCACGGACT); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES
KEYWDS DNA STRUCTURE, NOVEL DNA BASES, ANTISENSE OLIGONUCLEOTIDES, KEYWDS 2 INTERCALATOR BINDING, REVERSE WATSON-CRICK BASE PAIRS, KEYWDS 3 DEOXYRIBONUCLEIC ACID
EXPDTA SOLUTION NMR
AUTHOR X.-L.YANG,H.SUGIYAMA,S.IKEDA,I.SAITO,A.H.-J.WANG
REVDAT 3 24-FEB-09 1BE5 1 VERSN REVDAT 2 01-APR-03 1BE5 1 JRNL REVDAT 1 12-AUG-98 1BE5 0
JRNL AUTH X.L.YANG,H.SUGIYAMA,S.IKEDA,I.SAITO,A.H.WANG JRNL TITL STRUCTURAL STUDIES OF A STABLE PARALLEL-STRANDED JRNL TITL 2 DNA DUPLEX INCORPORATING ISOGUANINE:CYTOSINE AND JRNL TITL 3 ISOCYTOSINE:GUANINE BASEPAIRS BY NUCLEAR MAGNETIC JRNL TITL 4 RESONANCE SPECTROSCOPY. JRNL REF BIOPHYS.J. V. 75 1163 1998 JRNL REFN ISSN 0006-3495 JRNL PMID 9726918
REMARK 1
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: REFINEMENT DETAILS CAN BE FOUND IN REMARK 3 THE JRNL CITATION ABOVE.
REMARK 4 REMARK 4 1BE5 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) : 275 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 20MM PHOSPHATE BUFFER REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : WATER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY, TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ, 500 MHZ REMARK 210 SPECTROMETER MODEL : UNITY 750, VXR 500 REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR, SPEDREF REMARK 210 METHOD USED : NOE-RMD REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : MINIMIZED AVERAGE REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING 1H 2D NMR REMARK 210 SPECTROSCOPY
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 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 C5' DT A 1 C4' 0.069 REMARK 500 DT A 1 C5 DT A 1 C7 0.042 REMARK 500 DT A 10 C5 DT A 10 C7 0.042 REMARK 500 DG B 13 C3' DG B 13 C2' -0.048 REMARK 500 DT B 14 C5' DT B 14 C4' 0.067 REMARK 500 DT B 14 C5 DT B 14 C7 0.039 REMARK 500 DC B 16 C5' DC B 16 C4' 0.055 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' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DA A 4 N9 - C4 - C5 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA A 8 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 DG B 15 O4' - C4' - C3' ANGL. DEV. = 5.3 DEGREES REMARK 500 DG B 15 C4' - C3' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 DC B 17 O4' - C1' - N1 ANGL. DEV. = -5.9 DEGREES REMARK 500 DG B 19 C4' - C3' - C2' ANGL. DEV. = -5.9 DEGREES REMARK 500 DG B 19 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 DA B 20 O4' - C1' - N9 ANGL. DEV. = 2.1 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 DT A 10 0.10 SIDE_CHAIN REMARK 500 DG B 15 0.10 SIDE_CHAIN REMARK 500 DA B 20 0.09 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
DBREF 1BE5 A 1 10 PDB 1BE5 1BE5 1 10 DBREF 1BE5 B 11 20 PDB 1BE5 1BE5 11 20
SEQRES 1 A 10 DT IGU IMC DA IMC IGU IGU DA IMC DT SEQRES 1 B 10 DA DC DG DT DG DC DC DT DG DA
MODRES 1BE5 IGU A 2 DG 2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE MODRES 1BE5 IMC A 3 DC MODRES 1BE5 IMC A 5 DC MODRES 1BE5 IGU A 6 DG 2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE MODRES 1BE5 IGU A 7 DG 2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE MODRES 1BE5 IMC A 9 DC
HET IGU A 2 33 HET IMC A 3 33 HET IMC A 5 33 HET IGU A 6 33 HET IGU A 7 33 HET IMC A 9 33
HETNAM IGU 2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE HETNAM IMC N1-[2-DEOXY-RIBOFURANOSYL]-[2-AMINO-5-METHYL-4-OXO-4H- HETNAM 2 IMC PYRIMIDINE]-5'-MONOPHOSPHATE
FORMUL 1 IGU 3(C10 H14 N5 O7 P) FORMUL 1 IMC 3(C10 H16 N3 O7 P)
LINK P IGU A 2 O3' DT A 1 1555 1555 1.61 LINK O3' IGU A 2 P IMC A 3 1555 1555 1.63 LINK O3' IMC A 3 P DA A 4 1555 1555 1.61 LINK P IMC A 5 O3' DA A 4 1555 1555 1.63 LINK O3' IMC A 5 P IGU A 6 1555 1555 1.62 LINK O3' IGU A 6 P IGU A 7 1555 1555 1.62 LINK O3' IGU A 7 P DA A 8 1555 1555 1.62 LINK P IMC A 9 O3' DA A 8 1555 1555 1.63 LINK O3' IMC A 9 P DT A 10 1555 1555 1.63
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