HEADER DNA 30-OCT-02 1N4B TITLE SOLUTION STRUCTURE OF THE UNDECAMER CGAAAC*TTTCG COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*AP*AP*AP*CP*TP*TP*TP*CP*G)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: INTERSTRAND CROSS-LINKED DNA; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*CP*GP*AP*AP*AP*D00*TP*TP*TP*CP*G)-3'; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: INTERSTRAND CROSS-LINKED DNA SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS INTERSTRAND CROSS-LINK, ALKYLATED DNA, MODIFIED CYTOSINE, ALKYLATED KEYWDS 2 CYTOSINE, DNA EXPDTA SOLUTION NMR AUTHOR M.WEBBA DA SILVA,A.M.NORONHA,D.M.NOLL,P.S.MILLER,O.M.COLVIN, AUTHOR 2 M.P.GAMCSIK REVDAT 3 25-JUN-14 1N4B 1 HETNAM REVDAT 2 24-FEB-09 1N4B 1 VERSN REVDAT 1 04-NOV-03 1N4B 0 JRNL AUTH M.WEBBA DA SILVA,A.M.NORONHA,D.M.NOLL,P.S.MILLER,O.M.COLVIN, JRNL AUTH 2 M.P.GAMCSIK JRNL TITL SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING JRNL TITL 2 MISPAIR-ALIGNED N4C-ETHYL-N4C INTERSTRAND CROSS-LINKED JRNL TITL 3 CYTOSINES JRNL REF BIOCHEMISTRY V. 41 15181 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 12484755 JRNL DOI 10.1021/BI026368L REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.8 REMARK 3 AUTHORS : BRUNGER, A.T. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 A TOTAL OF 449 RESTRAINTS WERE USED REMARK 3 243 NON-EXCHANGEABLE REMARK 3 53 EXCHANGEABLE REMARK 3 44 HYDROGEN BOND REMARK 3 109 DIHEDRAL ANGLE REMARK 4 REMARK 4 1N4B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-NOV-02. REMARK 100 THE RCSB ID CODE IS RCSB017501. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293; 273 REMARK 210 PH : 7.4; 7.4 REMARK 210 IONIC STRENGTH : 100 MM NACL; 100 MM NACL REMARK 210 PRESSURE : NORMAL; NORMAL REMARK 210 SAMPLE CONTENTS : THE SYNTHESIS BY SOLID PHASE REMARK 210 METHODS OF DNA DUPLEXES THAT REMARK 210 CONTAIN AN N4-C-ETHYL-N4C REMARK 210 INTERSTRAND CROSS-LINK HAS BEEN REMARK 210 DESCRIBED [BIOCHEMISTRY,41(2002) REMARK 210 760-771]. 2 MM SINGLE STRAND REMARK 210 CONCENTRATION IN 0.3 ML REMARK 210 CONTAINING 10 MM SODIUM PHOSPHATE REMARK 210 (PH 7.4) AND 100 MM NACL. REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : THE STRUCTURE SUBMITTED IS THE REMARK 210 LOWEST ENERGY STRUCTURE OF A AN REMARK 210 ENSEMBLE OF SELECTED TEN REMARK 210 STRUCTURES REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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 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 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 D00 B 6 C2 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 N4 DC A 6 C10 D00 B 6 1.47 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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG A 2 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = -4.7 DEGREES REMARK 500 DA A 3 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA A 4 C1' - O4' - C4' ANGL. DEV. = -7.8 DEGREES REMARK 500 DA A 4 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES REMARK 500 DA A 4 O4' - C1' - C2' ANGL. DEV. = -10.9 DEGREES REMARK 500 DC A 6 O4' - C1' - C2' ANGL. DEV. = -11.1 DEGREES REMARK 500 DC A 6 O4' - C1' - N1 ANGL. DEV. = -7.1 DEGREES REMARK 500 DC A 6 C2 - N3 - C4 ANGL. DEV. = 4.6 DEGREES REMARK 500 DC A 6 N3 - C4 - C5 ANGL. DEV. = -5.3 DEGREES REMARK 500 DT A 7 O4' - C1' - C2' ANGL. DEV. = -9.4 DEGREES REMARK 500 DT A 7 C4 - C5 - C6 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT A 7 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 DT A 8 O4' - C1' - C2' ANGL. DEV. = -9.8 DEGREES REMARK 500 DT A 9 C5' - C4' - O4' ANGL. DEV. = 7.9 DEGREES REMARK 500 DT A 9 O4' - C1' - C2' ANGL. DEV. = -10.6 DEGREES REMARK 500 DT A 9 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DC A 10 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 DC A 10 O4' - C1' - C2' ANGL. DEV. = -13.0 DEGREES REMARK 500 DC A 10 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG A 11 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 DC B 1 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG B 2 O4' - C1' - C2' ANGL. DEV. = -5.7 DEGREES REMARK 500 DG B 2 O4' - C1' - N9 ANGL. DEV. = -4.9 DEGREES REMARK 500 DA B 3 C4' - C3' - C2' ANGL. DEV. = -4.4 DEGREES REMARK 500 DA B 3 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA B 4 C1' - O4' - C4' ANGL. DEV. = -7.3 DEGREES REMARK 500 DA B 4 O4' - C1' - C2' ANGL. DEV. = -11.4 DEGREES REMARK 500 DT B 7 O4' - C1' - C2' ANGL. DEV. = -9.8 DEGREES REMARK 500 DT B 7 C4 - C5 - C6 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT B 7 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 DT B 8 O4' - C1' - C2' ANGL. DEV. = -10.4 DEGREES REMARK 500 DT B 8 C4 - C5 - C6 ANGL. DEV. = 3.6 DEGREES REMARK 500 DT B 9 C5' - C4' - O4' ANGL. DEV. = 7.6 DEGREES REMARK 500 DT B 9 O4' - C1' - C2' ANGL. DEV. = -11.1 DEGREES REMARK 500 DT B 9 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DC B 10 C4' - C3' - O3' ANGL. DEV. = 12.1 DEGREES REMARK 500 DC B 10 O4' - C1' - C2' ANGL. DEV. = -13.3 DEGREES REMARK 500 DC B 10 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG B 11 O4' - C4' - C3' ANGL. DEV. = -3.1 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 DC A 6 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 DA A 4 -46.3 D D OUTSIDE RANGE REMARK 500 DC A 10 -45.9 D D OUTSIDE RANGE REMARK 500 DA B 4 -47.3 D D OUTSIDE RANGE REMARK 500 DT B 8 -46.1 D D OUTSIDE RANGE REMARK 500 DC B 10 -46.5 D D OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL DBREF 1N4B A 1 11 PDB 1N4B 1N4B 1 11 DBREF 1N4B B 1 11 PDB 1N4B 1N4B 1 11 SEQRES 1 A 11 DC DG DA DA DA DC DT DT DT DC DG SEQRES 1 B 11 DC DG DA DA DA D00 DT DT DT DC DG MODRES 1N4B D00 B 6 DC HET D00 B 6 33 HETNAM D00 2'-DEOXY-N-ETHYLCYTIDINE 5'-(DIHYDROGEN PHOSPHATE) FORMUL 2 D00 C11 H18 N3 O7 P LINK O3' DA B 5 P D00 B 6 1555 1555 1.61 LINK O3' D00 B 6 P DT B 7 1555 1555 1.60 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