PDB Short entry for 2KTP HEADER DNA 05-FEB-10 2KTP TITLE STRUCTURE OF THE 1,N2-ETHENODEOXYGUANOSINE LESION OPPOSITE A ONE-BASE TITLE 2 DELETION IN DUPLEX DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*AP*TP*(GNE)P*GP*AP*AP*TP*CP*C)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*GP*GP*AP*TP*TP*CP*AP*TP*GP*CP*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 ETHENOGUANINE, ONE-BASE DELETION, DNA EXPDTA SOLUTION NMR AUTHOR G.SHANMUGAM,I.D.KOZEKOV,P.F.GUENGERICH,C.J.RIZZO,M.P.STONE REVDAT 3 16-MAR-22 2KTP 1 REMARK LINK REVDAT 2 26-MAY-10 2KTP 1 JRNL REVDAT 1 23-MAR-10 2KTP 0 JRNL AUTH G.SHANMUGAM,I.D.KOZEKOV,F.P.GUENGERICH,C.J.RIZZO,M.P.STONE JRNL TITL STRUCTURE OF THE 1,N(2)-ETHENO-2'-DEOXYGUANOSINE LESION IN JRNL TITL 2 THE 3'-G(EPSILON DG)T-5' SEQUENCE OPPOSITE A ONE-BASE JRNL TITL 3 DELETION. JRNL REF BIOCHEMISTRY V. 49 2615 2010 JRNL REFN ISSN 0006-2960 JRNL PMID 20201499 JRNL DOI 10.1021/BI901516D REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO AND KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KTP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1000101561. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.3 MM DNA (5' REMARK 210 -D(P*GP*CP*AP*TP*GP*GP*AP*AP*TP*C)-3')-1, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H COSY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM 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 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 DG A 2 N3 DG A 2 C4 0.066 REMARK 500 DG A 2 C5 DG A 2 C6 0.088 REMARK 500 DG A 2 N7 DG A 2 C8 0.102 REMARK 500 DA A 4 N3 DA A 4 C4 0.060 REMARK 500 DA A 4 N7 DA A 4 C8 0.095 REMARK 500 DG A 7 N3 DG A 7 C4 0.067 REMARK 500 DG A 7 C5 DG A 7 C6 0.082 REMARK 500 DG A 7 N7 DG A 7 C8 0.100 REMARK 500 DA A 8 N3 DA A 8 C4 0.066 REMARK 500 DA A 8 N7 DA A 8 C8 0.094 REMARK 500 DA A 9 N3 DA A 9 C4 0.062 REMARK 500 DA A 9 N7 DA A 9 C8 0.094 REMARK 500 DG B 13 N3 DG B 13 C4 0.065 REMARK 500 DG B 13 C5 DG B 13 C6 0.085 REMARK 500 DG B 13 N7 DG B 13 C8 0.101 REMARK 500 DG B 14 N3 DG B 14 C4 0.070 REMARK 500 DG B 14 C5 DG B 14 C6 0.084 REMARK 500 DG B 14 N7 DG B 14 C8 0.102 REMARK 500 DA B 15 N3 DA B 15 C4 0.061 REMARK 500 DA B 15 N7 DA B 15 C8 0.092 REMARK 500 DA B 19 N3 DA B 19 C4 0.064 REMARK 500 DA B 19 N7 DA B 19 C8 0.094 REMARK 500 DG B 21 N3 DG B 21 C4 0.067 REMARK 500 DG B 21 C5 DG B 21 C6 0.088 REMARK 500 DG B 21 N7 DG B 21 C8 0.104 REMARK 500 DG B 23 N3 DG B 23 C4 0.068 REMARK 500 DG B 23 C5 DG B 23 C6 0.084 REMARK 500 DG B 23 N7 DG B 23 C8 0.102 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 N1 - C2 - O2 ANGL. DEV. = 4.9 DEGREES REMARK 500 DC A 1 N3 - C2 - O2 ANGL. DEV. = -6.0 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG A 2 N3 - C4 - C5 ANGL. DEV. = -4.5 DEGREES REMARK 500 DG A 2 C5 - N7 - C8 ANGL. DEV. = -3.4 DEGREES REMARK 500 DC A 3 N1 - C2 - O2 ANGL. DEV. = 5.0 DEGREES REMARK 500 DC A 3 N3 - C2 - O2 ANGL. DEV. = -6.0 DEGREES REMARK 500 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 DA A 4 C5 - C6 - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 DT A 5 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DT A 5 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 DT A 5 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DG A 7 N3 - C4 - C5 ANGL. DEV. = -4.3 DEGREES REMARK 500 DA A 8 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA A 8 C5 - C6 - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DA A 8 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 DA A 9 C5 - C6 - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DA A 9 N9 - C4 - C5 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA A 9 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT A 10 OP1 - P - OP2 ANGL. DEV. = -9.2 DEGREES REMARK 500 DT A 10 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT A 10 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 DT A 10 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DC A 11 N1 - C2 - O2 ANGL. DEV. = 4.3 DEGREES REMARK 500 DC A 11 N3 - C2 - O2 ANGL. DEV. = -6.0 DEGREES REMARK 500 DC A 12 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 DC A 12 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG B 13 N3 - C4 - C5 ANGL. DEV. = -4.6 DEGREES REMARK 500 DG B 13 C5 - N7 - C8 ANGL. DEV. = -3.1 DEGREES REMARK 500 DG B 14 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG B 14 N3 - C4 - C5 ANGL. DEV. = -4.7 DEGREES REMARK 500 DG B 14 C5 - N7 - C8 ANGL. DEV. = -3.3 DEGREES REMARK 500 DA B 15 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA B 15 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA B 15 N9 - C4 - C5 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA B 15 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 DT B 16 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DT B 16 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 DT B 17 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT B 17 N3 - C2 - O2 ANGL. DEV. = -3.9 DEGREES REMARK 500 DC B 18 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC B 18 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC B 18 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 DA B 19 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 DA B 19 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA B 19 N9 - C4 - C5 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA B 19 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 62 ANGLE DEVIATIONS. 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 DT A 10 0.08 SIDE CHAIN REMARK 500 DA B 15 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2KTP A 1 12 PDB 2KTP 2KTP 1 12 DBREF 2KTP B 13 23 PDB 2KTP 2KTP 13 23 SEQRES 1 A 12 DC DG DC DA DT GNE DG DA DA DT DC DC SEQRES 1 B 11 DG DG DA DT DT DC DA DT DG DC DG HET GNE A 6 35 HETNAM GNE 1,N2-ETHENOGUANINE FORMUL 1 GNE C12 H14 N5 O7 P LINK O3' DT A 5 P GNE A 6 1555 1555 1.64 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