HEADER DNA BINDING PROTEIN/DNA 08-MAR-10 2KV6 TITLE TETRAPEPTIDE KWKK CONJUGATED TO OLIGONUCLEOTIDE DUPLEX BY A TITLE 2 TRIMETHYLENE TETHER COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*GP*AP*CP*TP*CP*GP*CP*TP*AP*GP*C)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: KWKK TETRAPEPTIDE; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 SYNTHETIC: YES KEYWDS DNA-PEPTIDE CONJUGATE, TRIMETHYLENE, ACROLEIN-DG ADDUCT, DNA-PEPTIDE KEYWDS 2 COMPLEX, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA SOLUTION NMR AUTHOR H.HUANG,I.D.KOZEKOV,A.KOZEKOVA,C.J.RIZZO,A.MCCULLOUGH,R.S.LLOYD, AUTHOR 2 M.P.STONE REVDAT 2 11-AUG-10 2KV6 1 JRNL REVDAT 1 21-JUL-10 2KV6 0 JRNL AUTH H.HUANG,I.D.KOZEKOV,A.KOZEKOVA,C.J.RIZZO,A.K.MCCULLOUGH, JRNL AUTH 2 R.S.LLOYD,M.P.STONE JRNL TITL MINOR GROOVE ORIENTATION OF THE KWKK PEPTIDE TETHERED VIA JRNL TITL 2 THE N-TERMINAL AMINE TO THE ACROLEIN-DERIVED JRNL TITL 3 1,N(2)-GAMMA-HYDROXYPROPANODEOXYGUANOSINE LESION WITH A JRNL TITL 4 TRIMETHYLENE LINKAGE . JRNL REF BIOCHEMISTRY V. 49 6155 2010 JRNL REFN ISSN 0006-2960 JRNL PMID 20604523 JRNL DOI 10.1021/BI100364F REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 7.0 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 2KV6 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAR-10. REMARK 100 THE RCSB ID CODE IS RCSB101612. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.3 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8 MM DNA (5'-D(*GP*CP*TP*AP* REMARK 210 GP*CP*GP*AP*GP*TP*CP*C)-3')-1, 0.8 MM DNA (5'-D(*GP*GP*AP*CP*TP* REMARK 210 CP*GP*CP*TP*AP*GP*C)-3')-2, 0.8 MM ENTITY_3-3, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H COSY; REMARK 210 2D 1H-1H TOCSY; 2D DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 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 : 10 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 2 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 DG A 5 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC A 6 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 DA A 8 C4 - C5 - C6 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA A 8 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA A 8 N1 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC A 11 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 DC A 12 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DA B 15 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 DA B 15 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA B 15 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 DC B 16 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC B 16 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 DT B 17 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 DC B 18 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC B 18 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 DC B 20 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC B 20 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 DT B 21 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT B 21 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA B 22 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 DA B 22 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA B 22 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 DC B 24 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC B 24 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC B 24 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 2KV6 A 1 12 PDB 2KV6 2KV6 1 12 DBREF 2KV6 B 13 24 PDB 2KV6 2KV6 13 24 DBREF 2KV6 C 26 29 PDB 2KV6 2KV6 26 29 SEQRES 1 A 12 DG DC DT DA DG DC 0AD DA DG DT DC DC SEQRES 1 B 12 DG DG DA DC DT DC DG DC DT DA DG DC SEQRES 1 C 4 LYS TRP LYS LYS MODRES 2KV6 0AD A 7 DG HET 0AD A 7 41 HETNAM 0AD 2'-DEOXY-N-PROPYLGUANOSINE 5'-(DIHYDROGEN PHOSPHATE) FORMUL 1 0AD C13 H20 N5 O7 P LINK C6A 0AD A 7 N LYS C 26 1555 1555 1.49 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