1XCI - Header Asymmetric Unit

HEADER DNA 02-SEP-04 1XCI

TITLE MISPAIR ALIGNED N3T-BUTYL-N3T INTERSTRAND CROSSLINK

COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*AP*AP*AP*(TTM)P*TP*TP*TP*CP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES

KEYWDS INTERSTRAND CROSS-LINK, DOUBLE HELIX, DNA

EXPDTA SOLUTION NMR

AUTHOR M.W.DA SILVA,R.G.BIERBRYER,C.J.WILDS,A.M.NORONHA,O.M.COLVIN, AUTHOR 2 P.S.MILLER,M.P.GAMCSIK

REVDAT 2 24-FEB-09 1XCI 1 VERSN REVDAT 1 16-AUG-05 1XCI 0

JRNL AUTH M.W.DA SILVA,R.G.BIERBRYER,C.J.WILDS,A.M.NORONHA, JRNL AUTH 2 O.M.COLVIN,P.S.MILLER,M.P.GAMCSIK JRNL TITL INTRASTRAND BASE-STACKING BUTTRESSES WIDENING OF JRNL TITL 2 MAJOR GROOVE IN INTERSTRAND CROSS-LINKED B-DNA. JRNL REF BIOORG.MED.CHEM. V. 13 4580 2005 JRNL REFN ISSN 0968-0896 JRNL PMID 15953553 JRNL DOI 10.1016/J.BMC.2005.03.032

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 2.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 1XCI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-SEP-04. REMARK 100 THE RCSB ID CODE IS RCSB030202.

REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 20; 0 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 : 1.5 MM SAMPLE IN 100 MM NACL, REMARK 210 50 MM PHOSPHATE PH 7.4, D2O; REMARK 210 1.5 MM SAMPLE IN 100 MM NACL, REMARK 210 50 MM PHOSPHATE PH 7.4, H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY, 2D TOCSY, 2D NOESY, REMARK 210 JR-NOESY, 31P,1H HETCOR REMARK 210 SPECTROMETER FIELD STRENGTH : 800 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 : 15 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: STRUCTURE DETERMINED USING STANDARD NMR 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 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 C4' - C3' - C2' ANGL. DEV. = -4.6 DEGREES REMARK 500 DC A 1 C3' - C2' - C1' ANGL. DEV. = -5.9 DEGREES REMARK 500 DA A 3 C3' - C2' - C1' ANGL. DEV. = -6.2 DEGREES REMARK 500 DA A 3 N1 - C6 - N6 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA A 4 C4' - C3' - C2' ANGL. DEV. = -4.5 DEGREES REMARK 500 DA A 4 C3' - C2' - C1' ANGL. DEV. = -8.0 DEGREES REMARK 500 DA A 4 O4' - C1' - C2' ANGL. DEV. = -6.5 DEGREES REMARK 500 DA A 4 O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 DA A 3 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 DA A 5 C3' - C2' - C1' ANGL. DEV. = -6.1 DEGREES REMARK 500 DA A 5 N1 - C6 - N6 ANGL. DEV. = 5.0 DEGREES REMARK 500 DT A 7 C4 - C5 - C6 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT A 7 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DT A 8 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 DT A 8 C4 - C5 - C6 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT A 8 C6 - C5 - C7 ANGL. DEV. = -5.8 DEGREES REMARK 500 DT A 9 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DT A 9 C3' - C2' - C1' ANGL. DEV. = -10.3 DEGREES REMARK 500 DT A 9 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 DT A 9 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT A 9 C4 - C5 - C6 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT A 9 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 DC A 10 C3' - C2' - C1' ANGL. DEV. = -6.2 DEGREES REMARK 500 DG A 11 O4' - C4' - C3' ANGL. DEV. = -3.6 DEGREES REMARK 500 DG A 11 C3' - C2' - C1' ANGL. DEV. = -8.4 DEGREES REMARK 500 DC B 1 C3' - C2' - C1' ANGL. DEV. = -6.6 DEGREES REMARK 500 DC B 1 O4' - C1' - C2' ANGL. DEV. = -5.8 DEGREES REMARK 500 DG B 2 O4' - C4' - C3' ANGL. DEV. = -3.1 DEGREES REMARK 500 DG B 2 C3' - C2' - C1' ANGL. DEV. = -10.6 DEGREES REMARK 500 DA B 3 C3' - C2' - C1' ANGL. DEV. = -6.5 DEGREES REMARK 500 DA B 3 N1 - C6 - N6 ANGL. DEV. = 4.4 DEGREES REMARK 500 DA B 4 C3' - C2' - C1' ANGL. DEV. = -9.1 DEGREES REMARK 500 DA B 4 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA B 3 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 DA B 5 C3' - C2' - C1' ANGL. DEV. = -7.2 DEGREES REMARK 500 DA B 5 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA B 5 N1 - C6 - N6 ANGL. DEV. = 4.7 DEGREES REMARK 500 DT B 7 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 DT B 8 C3' - C2' - C1' ANGL. DEV. = -5.7 DEGREES REMARK 500 DT B 8 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 DT B 8 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT B 9 C3' - C2' - C1' ANGL. DEV. = -9.5 DEGREES REMARK 500 DT B 9 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 DC B 10 C3' - C2' - C1' ANGL. DEV. = -6.9 DEGREES REMARK 500 DG B 11 O4' - C4' - C3' ANGL. DEV. = -3.7 DEGREES REMARK 500 DG B 11 C3' - C2' - C1' ANGL. DEV. = -9.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL

DBREF 1XCI A 1 11 PDB 1XCI 1XCI 1 11 DBREF 1XCI B 1 11 PDB 1XCI 1XCI 1 11

SEQRES 1 A 11 DC DG DA DA DA TTM DT DT DT DC DG SEQRES 1 B 11 DC DG DA DA DA TTM DT DT DT DC DG

MODRES 1XCI TTM A 6 DT N3-ETHYL-THYMIDINE-5'-MONOPHOSPHATE MODRES 1XCI TTM B 6 DT N3-ETHYL-THYMIDINE-5'-MONOPHOSPHATE

HET TTM A 6 37 HET TTM B 6 37

HETNAM TTM N3-ETHYL-THYMIDINE-5'-MONOPHOSPHATE

FORMUL 1 TTM 2(C12 H19 N2 O8 P)

LINK C2Q TTM A 6 C2Q TTM B 6 1555 1555 1.62 LINK O3' DA A 5 P TTM A 6 1555 1555 1.60 LINK O3' TTM A 6 P DT A 7 1555 1555 1.60 LINK O3' DA B 5 P TTM B 6 1555 1555 1.60 LINK O3' TTM 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