HEADER DNA 03-MAY-00 1EXL TITLE STRUCTURE OF AN 11-MER DNA DUPLEX CONTAINING THE CARBOCYCLIC TITLE 2 NUCLEOTIDE ANALOG: 2'-DEOXYARISTEROMYCIN CAVEAT 1EXL C3' OF G14 B HAS INCORRECT CHIRALITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (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 OTHER_DETAILS: DNA STRAND CONTAINING 2'-DEOXYARISTEROMYCIN-5'- COMPND 6 PHOSPHATE; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*GP*TP*GP*AP*CP*TP*CP*AP*CP*TP*G)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: 2'-DEOXYARISTEROMYCIN WAS CHEMICALLY SYNTHESIZED; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES KEYWDS DNA, MODIFIED NUCLEOTIDES, 2'-DEOXYARISTEROMYCIN EXPDTA SOLUTION NMR NUMMDL 30 MDLTYP MINIMIZED AVERAGE AUTHOR S.SMIRNOV,F.JOHNSON,R.MARUMOTO,C.DE LOS SANTOS REVDAT 5 01-MAY-24 1EXL 1 REMARK LINK REVDAT 4 28-DEC-11 1EXL 1 CAVEAT VERSN REVDAT 3 24-FEB-09 1EXL 1 VERSN REVDAT 2 21-DEC-04 1EXL 1 JRNL REMARK REVDAT 1 15-MAY-00 1EXL 0 JRNL AUTH S.SMIRNOV,F.JOHNSON,R.MARUMOTO,C.DE LOS SANTOS JRNL TITL STRUCTURE OF AN 11-MER DNA DUPLEX CONTAINING THE CARBOCYCLIC JRNL TITL 2 NUCLEOTIDE ANALOG: 2'-DEOXYARISTEROMYCIN JRNL REF J.BIOMOL.STRUCT.DYN. V. 17 981 2000 JRNL REFN ISSN 0739-1102 JRNL PMID 10949165 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX 95, X-PLOR 3.8 REMARK 3 AUTHORS : MSI (FELIX), BRUNGER, A. (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1EXL COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAY-00. REMARK 100 THE DEPOSITION ID IS D_1000010998. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 308 REMARK 210 PH : 6.9; 6.9 REMARK 210 IONIC STRENGTH : 50 MM NACL; 50 MM NACL REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 280 OD260 DNA; 10 MM PHOSPHATE REMARK 210 BUFFER; 50 MM NACL AND 1MM EDTA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MARDIGRAS 2.0, X-PLOR 3.8 REMARK 210 METHOD USED : MOLECULAR DYNAMICS; MATRIX REMARK 210 RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED, BACK CALCULATED DATA REMARK 210 AGREE WITH EXPERIMENTAL NOESY REMARK 210 SPECTRUM REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 15 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 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 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 1 DC A 1 C4 DC A 1 N4 0.106 REMARK 500 1 DA A 2 C6 DA A 2 N6 0.090 REMARK 500 1 DG A 3 C2 DG A 3 N2 0.080 REMARK 500 1 DT A 4 C3' DT A 4 C2' 0.122 REMARK 500 1 DT A 4 C2' DT A 4 C1' 0.137 REMARK 500 1 DG A 5 C2 DG A 5 N2 0.085 REMARK 500 1 DG A 7 C2 DG A 7 N2 0.090 REMARK 500 1 DC A 9 C2' DC A 9 C1' 0.074 REMARK 500 1 DC A 9 C4 DC A 9 N4 0.085 REMARK 500 1 DA A 10 C6 DA A 10 N6 0.101 REMARK 500 1 DC A 11 C4 DC A 11 N4 0.092 REMARK 500 1 DG B 12 C2 DG B 12 N2 0.082 REMARK 500 1 DG B 14 C2 DG B 14 N2 0.087 REMARK 500 1 DA B 15 C6 DA B 15 N6 0.083 REMARK 500 1 DC B 16 C4 DC B 16 N4 0.111 REMARK 500 1 DT B 17 C5 DT B 17 C7 0.050 REMARK 500 1 DC B 18 C4 DC B 18 N4 0.104 REMARK 500 1 DA B 19 C6 DA B 19 N6 0.091 REMARK 500 1 DC B 20 C4 DC B 20 N4 0.100 REMARK 500 1 DT B 21 C5 DT B 21 C7 0.041 REMARK 500 1 DG B 22 C2' DG B 22 C1' 0.098 REMARK 500 1 DG B 22 C2 DG B 22 N2 0.090 REMARK 500 2 DC A 1 C2' DC A 1 C1' 0.070 REMARK 500 2 DC A 1 C4 DC A 1 N4 0.109 REMARK 500 2 DA A 2 C6 DA A 2 N6 0.096 REMARK 500 2 DG A 3 C2 DG A 3 N2 0.085 REMARK 500 2 DT A 4 C3' DT A 4 C2' 0.110 REMARK 500 2 DT A 4 C2' DT A 4 C1' 0.159 REMARK 500 2 DG A 5 C8 DG A 5 N9 0.047 REMARK 500 2 DG A 5 C2 DG A 5 N2 0.084 REMARK 500 2 DG A 7 C2 DG A 7 N2 0.082 REMARK 500 2 DT A 8 C5 DT A 8 C7 0.052 REMARK 500 2 DC A 9 C3' DC A 9 C2' 0.085 REMARK 500 2 DC A 9 C2' DC A 9 C1' 0.135 REMARK 500 2 DC A 9 C4 DC A 9 N4 0.108 REMARK 500 2 DA A 10 C3' DA A 10 C2' 0.081 REMARK 500 2 DA A 10 C2' DA A 10 C1' 0.065 REMARK 500 2 DA A 10 C6 DA A 10 N6 0.103 REMARK 500 2 DC A 11 C2' DC A 11 C1' 0.071 REMARK 500 2 DC A 11 C4 DC A 11 N4 0.094 REMARK 500 2 DG B 12 C2 DG B 12 N2 0.082 REMARK 500 2 DG B 14 C2 DG B 14 N2 0.078 REMARK 500 2 DA B 15 C6 DA B 15 N6 0.093 REMARK 500 2 DC B 16 C4 DC B 16 N4 0.096 REMARK 500 2 DT B 17 C5 DT B 17 C7 0.047 REMARK 500 2 DC B 18 C2' DC B 18 C1' 0.067 REMARK 500 2 DC B 18 C4 DC B 18 N4 0.097 REMARK 500 2 DA B 19 C6 DA B 19 N6 0.093 REMARK 500 2 DC B 20 C4 DC B 20 N4 0.099 REMARK 500 2 DG B 22 C2' DG B 22 C1' 0.110 REMARK 500 REMARK 500 THIS ENTRY HAS 853 BOND DEVIATIONS. 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. = 1.9 DEGREES REMARK 500 1 DA A 2 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 1 DA A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DT A 4 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DT A 4 C5' - C4' - O4' ANGL. DEV. = 9.1 DEGREES REMARK 500 1 DT A 4 C1' - O4' - C4' ANGL. DEV. = 5.5 DEGREES REMARK 500 1 DT A 4 C4' - C3' - C2' ANGL. DEV. = -9.5 DEGREES REMARK 500 1 DT A 4 O4' - C1' - C2' ANGL. DEV. = -10.2 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DT A 4 C4 - C5 - C6 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 1 DG A 5 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DG A 5 C8 - N9 - C1' ANGL. DEV. = 9.4 DEGREES REMARK 500 1 DG A 7 C1' - O4' - C4' ANGL. DEV. = -6.7 DEGREES REMARK 500 1 DC A 9 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DA A 10 O4' - C4' - C3' ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DA A 10 C4' - C3' - C2' ANGL. DEV. = -6.0 DEGREES REMARK 500 1 DA A 10 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DA A 10 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DC A 11 O4' - C1' - C2' ANGL. DEV. = -9.2 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 8.0 DEGREES REMARK 500 1 DG B 12 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DG B 12 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG B 12 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DT B 13 C4' - C3' - C2' ANGL. DEV. = -7.7 DEGREES REMARK 500 1 DT B 13 O4' - C1' - C2' ANGL. DEV. = -7.5 DEGREES REMARK 500 1 DT B 13 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 1 DG B 14 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DG B 14 C3' - C2' - C1' ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DG B 14 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 1 DG B 14 C8 - N9 - C1' ANGL. DEV. = 7.9 DEGREES REMARK 500 1 DA B 15 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DA B 15 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 DT B 17 C5 - C6 - N1 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DT B 17 C3' - O3' - P ANGL. DEV. = 10.0 DEGREES REMARK 500 1 DC B 18 N1 - C1' - C2' ANGL. DEV. = 8.8 DEGREES REMARK 500 1 DC B 18 O4' - C1' - N1 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DA B 19 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DC B 20 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DT B 21 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DT B 21 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DG B 22 O4' - C4' - C3' ANGL. DEV. = -2.8 DEGREES REMARK 500 1 DG B 22 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG B 22 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 2 DA A 2 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 2 DA A 2 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 DA A 2 C8 - N9 - C4 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DG A 3 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 2 DT A 4 O4' - C4' - C3' ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DT A 4 C5' - C4' - O4' ANGL. DEV. = 8.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 1400 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1EXL A 1 11 PDB 1EXL 1EXL 1 11 DBREF 1EXL B 12 22 PDB 1EXL 1EXL 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 DT DC DA DC DT DG MODRES 1EXL 2AR A 6 DA 2'-DEOXYARISTEROMYCIN-5'-PHOSPHATE HET 2AR A 6 34 HETNAM 2AR 2'-DEOXYARISTEROMYCIN-5'-PHOSPHATE HETSYN 2AR [ADENIN-9-YL-3-HYDROXY-CYCLOPENTAN-5-YL]-METHYL-5'- HETSYN 2 2AR PHOSPHATE FORMUL 1 2AR C11 H16 N5 O5 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 1.61 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 MODEL 1