PDB Short entry for 1XCI 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; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 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 4 01-MAY-24 1XCI 1 LINK REVDAT 3 06-JUN-18 1XCI 1 SOURCE REMARK 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,O.M.COLVIN, JRNL AUTH 2 P.S.MILLER,M.P.GAMCSIK JRNL TITL INTRASTRAND BASE-STACKING BUTTRESSES WIDENING OF MAJOR JRNL TITL 2 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 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. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-SEP-04. REMARK 100 THE DEPOSITION ID IS D_1000030202. 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 : 1.5 MM SAMPLE IN 100 MM NACL, 50 REMARK 210 MM PHOSPHATE PH 7.4, D2O; 1.5 MM REMARK 210 SAMPLE IN 100 MM NACL, 50 MM REMARK 210 PHOSPHATE PH 7.4, H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY; 2D TOCSY; 2D NOESY; JR REMARK 210 -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 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 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 3 C3' - O3' - P ANGL. DEV. = 8.1 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 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 3 C3' - O3' - P ANGL. DEV. = 7.5 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 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. = -5.8 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. = -9.4 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. = -3.8 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 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 C2Q TTM A 6 C2Q TTM B 6 1555 1555 1.62 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