10 20 30 40 50 60 70 80 1FYI - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 30-SEP-00 1FYI
TITLE 11-MER DNA DUPLEX CONTAINING A 2'-DEOXYARISTEROMYCIN 8-OXO- TITLE 2 GUANINE BASE PAIR;
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*AP*GP*TP*GP*(2AR)P*GP*TP*CP*AP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*TP*GP*AP*CP*(8OG)P*CP*AP*CP*TP*G)-3'; 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 2'-DEOXYARISTEROMYCIN, 8-OXO-GUANINE, DNA
EXPDTA SOLUTION NMR
NUMMDL 9
AUTHOR S.SMIRNOV,F.JOHNSON,C.DE LOS SANTOS
REVDAT 2 24-FEB-09 1FYI 1 VERSN REVDAT 1 18-OCT-00 1FYI 0
JRNL AUTH S.SMIRNOV,F.JOHNSON,C.DE LOS SANTOS JRNL TITL STRUCTURAL NMR CHARACTERIZATION OF AN 11-MER DNA JRNL TITL 2 DUPLEX CONTAINING A 2'-DEOXYARISTEROMYCIN JRNL TITL 3 8-OXO-GUANINE PAIR, NONHYDROLYZABLE SUBSTRATE JRNL TITL 4 ANALOG FOR THE DNA REPAIR ENZYME MUTY JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.8 REMARK 3 AUTHORS : A. BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1FYI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-OCT-00. REMARK 100 THE RCSB ID CODE IS RCSB012016.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 284; 298 REMARK 210 PH : 6.8; 6.8 REMARK 210 IONIC STRENGTH : 50MM; 50MM REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 280 OD260 IN 0.6 ML OF 50 MM REMARK 210 PHOSPHATE BUFFER, PH 6.8; 280 REMARK 210 OD260 IN 0.6 ML OF 50 MM REMARK 210 PHOSPHATE BUFFER, PH 6.8 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, DQF-COSY, TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 5, FELIX 95 REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 15 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 9 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 4 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O2 DC A 11 N2 DG B 12 2.02 REMARK 500 N3 DC A 11 N2 DG B 12 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 5 DT B 13 O3' DG B 14 P 0.136 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 1 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DA A 2 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA A 2 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG A 3 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DG A 5 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 5 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DG A 7 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DG A 7 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DC A 9 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DA A 10 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DG B 12 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG B 12 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DT B 13 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DG B 14 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG B 14 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG B 14 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DA B 15 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DA B 15 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DC B 16 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DC B 18 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DA B 19 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DA B 19 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC B 20 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DT B 21 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DG B 22 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG B 22 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG B 22 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DA A 2 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DA A 2 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DG A 3 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DG A 5 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 DG A 5 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DG A 7 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 DG A 7 C8 - N9 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 DT A 8 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DC A 9 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DA A 10 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DG B 12 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 302 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EXL RELATED DB: PDB REMARK 900 11-MER DNA DUPLEX CONTAINING THE CARBOCYCLIC NUCLEOTIDE REMARK 900 ANALOG: 2'-DEOXYARISTEROMYCIN
DBREF 1FYI A 1 11 PDB 1FYI 1FYI 1 11 DBREF 1FYI B 12 22 PDB 1FYI 1FYI 12 22
SEQRES 1 A 11 DC DA DG DT DG 2AR DG DT DC DA DC SEQRES 1 B 11 DG DT DG DA DC 8OG DC DA DC DT DG
MODRES 1FYI 2AR A 6 DA 2'-DEOXYARISTEROMYCIN-5'-PHOSPHATE MODRES 1FYI 8OG B 17 DG
HET 2AR A 6 34 HET 8OG B 17 34
HETNAM 2AR 2'-DEOXYARISTEROMYCIN-5'-PHOSPHATE HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
HETSYN 2AR [ADENIN-9-YL-3-HYDROXY-CYCLOPENTAN-5-YL]-METHYL-5'- HETSYN 2 2AR PHOSPHATE HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
FORMUL 1 2AR C11 H16 N5 O5 P FORMUL 2 8OG C10 H14 N5 O8 P
LINK O3' DG A 5 P 2AR A 6 1555 1555 1.62 LINK O3' 2AR A 6 P DG A 7 1555 1555 1.62 LINK O3' DC B 16 P 8OG B 17 1555 1555 1.61 LINK O3' 8OG B 17 P DC B 18 1555 1555 1.61
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