HEADER DNA 14-OCT-02 1G5K TITLE NMR STRUCTRURE OF D(CCAAAGXACTGGG), X IS A 3'-PHOSPHOGLYCOLATE, 5'- TITLE 2 PHOSPHATE GAPPED LESION, 10 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*AP*AP*AP*G)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(P*AP*CP*TP*GP*GP*G)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: 5'-D(*CP*CP*CP*AP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3'; 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, BLEOMYCIN, PHOSPHOGLYCOLATE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR H.-D.JUNKER,S.T.HOEHN,R.C.BUNT,V.MARATHIUS,J.CHEN,C.J.TURNER,J.STUBBE REVDAT 3 23-FEB-22 1G5K 1 REMARK LINK REVDAT 2 24-FEB-09 1G5K 1 VERSN REVDAT 1 07-JAN-03 1G5K 0 JRNL AUTH H.-D.JUNKER,S.T.HOEHN,R.C.BUNT,V.MARATHIUS,J.CHEN, JRNL AUTH 2 C.J.TURNER,J.STUBBE JRNL TITL SYNTHESIS, CHARACTERIZATION AND SOLUTION STRUCTURE OF JRNL TITL 2 TETHERED OLIGONUCLEOTIDES CONTAINING AN INTERNAL JRNL TITL 3 3'-PHOSPHOGLYCOLATE, 5'-PHOSPHATE GAPPED LESION JRNL REF NUCLEIC ACIDS RES. V. 30 5497 2002 JRNL REFN ISSN 0305-1048 JRNL PMID 12490718 JRNL DOI 10.1093/NAR/GKF681 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1G5K COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-NOV-02. REMARK 100 THE DEPOSITION ID IS D_1000017373. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293.15 REMARK 210 PH : 6.9 REMARK 210 IONIC STRENGTH : 40 MM NAHPO4 REMARK 210 PRESSURE : 1.0 ATM REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : PECOSY; TOCSY; NOESY; HSQC; GE REMARK 210 -HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : CUSTOM BUILD REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XPLOR 3.851 REMARK 210 METHOD USED : CONJUGATE GRADIENT MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : MINIMUM RMSD AND NMR CONSTRAINTS REMARK 210 VIOLATION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 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 1 DA B 8 P DA B 8 OP3 -0.124 REMARK 500 1 DT C 19 C5' DT C 19 C4' 0.044 REMARK 500 1 DA C 20 C5' DA C 20 C4' 0.046 REMARK 500 1 DT C 23 C5' DT C 23 C4' 0.043 REMARK 500 2 DA B 8 P DA B 8 OP3 -0.124 REMARK 500 2 DG B 11 C5' DG B 11 C4' 0.044 REMARK 500 2 DA C 20 C5' DA C 20 C4' 0.052 REMARK 500 2 DT C 22 C5' DT C 22 C4' 0.042 REMARK 500 2 DT C 23 C5' DT C 23 C4' 0.044 REMARK 500 3 DA B 8 P DA B 8 OP3 -0.121 REMARK 500 3 DT B 10 N1 DT B 10 C2 0.049 REMARK 500 3 DC C 21 C5' DC C 21 C4' 0.042 REMARK 500 3 DT C 22 C5' DT C 22 C4' 0.044 REMARK 500 4 DA A 3 C5' DA A 3 C4' 0.044 REMARK 500 4 DA B 8 P DA B 8 OP3 -0.124 REMARK 500 4 DG B 11 C5' DG B 11 C4' 0.044 REMARK 500 4 DT C 19 C5' DT C 19 C4' 0.046 REMARK 500 4 DT C 22 C5' DT C 22 C4' 0.046 REMARK 500 4 DT C 22 N1 DT C 22 C2 0.052 REMARK 500 5 DA B 8 P DA B 8 OP3 -0.130 REMARK 500 5 DC C 21 C5' DC C 21 C4' 0.042 REMARK 500 5 DT C 22 C5' DT C 22 C4' 0.044 REMARK 500 6 DA A 3 C5' DA A 3 C4' 0.045 REMARK 500 6 DA A 4 C5' DA A 4 C4' 0.044 REMARK 500 6 DA B 8 P DA B 8 OP3 -0.124 REMARK 500 6 DT C 19 N1 DT C 19 C2 0.048 REMARK 500 6 DT C 22 C5' DT C 22 C4' 0.042 REMARK 500 7 DA A 3 C5' DA A 3 C4' 0.048 REMARK 500 7 DA B 8 P DA B 8 OP3 -0.122 REMARK 500 7 DG B 11 C5' DG B 11 C4' 0.044 REMARK 500 7 DT C 19 C5' DT C 19 C4' 0.045 REMARK 500 7 DC C 21 C5' DC C 21 C4' 0.042 REMARK 500 7 DT C 22 C5' DT C 22 C4' 0.051 REMARK 500 7 DT C 22 N1 DT C 22 C2 0.053 REMARK 500 8 DA B 8 P DA B 8 OP3 -0.124 REMARK 500 8 DT C 22 C5' DT C 22 C4' 0.045 REMARK 500 8 DT C 23 C5' DT C 23 C4' 0.044 REMARK 500 9 DA B 8 P DA B 8 OP3 -0.125 REMARK 500 9 DG B 11 C5' DG B 11 C4' 0.043 REMARK 500 9 DT C 19 C5' DT C 19 C4' 0.047 REMARK 500 9 DA C 20 C5' DA C 20 C4' 0.042 REMARK 500 9 DT C 22 C5' DT C 22 C4' 0.043 REMARK 500 9 DT C 22 N1 DT C 22 C2 0.051 REMARK 500 10 DA B 8 P DA B 8 OP3 -0.130 REMARK 500 10 DC C 21 C5' DC C 21 C4' 0.044 REMARK 500 10 DT C 22 C5' DT C 22 C4' 0.045 REMARK 500 10 DT C 23 C5' DT C 23 C4' 0.042 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 1 DC A 2 C3' - O3' - P ANGL. DEV. = 8.5 DEGREES REMARK 500 1 DA A 4 N1 - C6 - N6 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DA A 5 N1 - C6 - N6 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG A 6 N3 - C2 - N2 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DA B 8 N1 - C6 - N6 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DT B 10 C3' - O3' - P ANGL. DEV. = 11.2 DEGREES REMARK 500 1 DG B 11 N3 - C2 - N2 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DG B 12 N3 - C2 - N2 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DG B 13 N3 - C2 - N2 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DC C 14 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC C 21 C3' - O3' - P ANGL. DEV. = 8.5 DEGREES REMARK 500 1 DT C 24 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 1 DG C 26 N3 - C2 - N2 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 DC A 2 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 2 DA A 4 N1 - C6 - N6 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 DA A 5 N1 - C6 - N6 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 DG A 6 N3 - C2 - N2 ANGL. DEV. = 5.5 DEGREES REMARK 500 2 DA B 8 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DC B 9 N3 - C4 - N4 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 DG B 11 N3 - C2 - N2 ANGL. DEV. = 7.2 DEGREES REMARK 500 2 DG B 12 N3 - C2 - N2 ANGL. DEV. = 5.7 DEGREES REMARK 500 2 DG B 13 N3 - C2 - N2 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 DA C 17 N1 - C6 - N6 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DG C 18 C2 - N3 - C4 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DC C 21 C3' - O3' - P ANGL. DEV. = 7.9 DEGREES REMARK 500 2 DG C 25 N3 - C2 - N2 ANGL. DEV. = 6.6 DEGREES REMARK 500 2 DG C 26 N3 - C2 - N2 ANGL. DEV. = 5.0 DEGREES REMARK 500 3 DC A 2 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 DA A 4 N1 - C6 - N6 ANGL. DEV. = 5.0 DEGREES REMARK 500 3 DA A 5 N1 - C6 - N6 ANGL. DEV. = 5.0 DEGREES REMARK 500 3 DG A 6 N3 - C2 - N2 ANGL. DEV. = 5.8 DEGREES REMARK 500 3 DA B 8 N1 - C6 - N6 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 DT B 10 C3' - O3' - P ANGL. DEV. = 8.6 DEGREES REMARK 500 3 DG B 11 N3 - C2 - N2 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 DG B 12 N3 - C2 - N2 ANGL. DEV. = 6.2 DEGREES REMARK 500 3 DG B 13 N3 - C2 - N2 ANGL. DEV. = 4.8 DEGREES REMARK 500 3 DG C 18 N3 - C2 - N2 ANGL. DEV. = 5.0 DEGREES REMARK 500 3 DT C 22 C3' - O3' - P ANGL. DEV. = 8.6 DEGREES REMARK 500 3 DT C 23 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 3 DG C 26 N3 - C2 - N2 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 DA A 3 N1 - C6 - N6 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 DA A 4 N1 - C6 - N6 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 DA A 5 N1 - C6 - N6 ANGL. DEV. = 5.7 DEGREES REMARK 500 4 DA A 5 C5 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 4 DG A 6 N3 - C2 - N2 ANGL. DEV. = 7.0 DEGREES REMARK 500 4 DA B 8 N1 - C6 - N6 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 DG B 12 N3 - C2 - N2 ANGL. DEV. = 5.8 DEGREES REMARK 500 4 DG B 13 N3 - C2 - N2 ANGL. DEV. = 4.9 DEGREES REMARK 500 4 DA C 17 N1 - C6 - N6 ANGL. DEV. = 4.7 DEGREES REMARK 500 4 DG C 18 N3 - C2 - N2 ANGL. DEV. = 5.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 128 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 1 DG A 6 0.06 SIDE CHAIN REMARK 500 1 DC B 9 0.10 SIDE CHAIN REMARK 500 1 DG B 13 0.09 SIDE CHAIN REMARK 500 1 DA C 20 0.05 SIDE CHAIN REMARK 500 1 DT C 22 0.09 SIDE CHAIN REMARK 500 1 DT C 23 0.10 SIDE CHAIN REMARK 500 1 DG C 25 0.07 SIDE CHAIN REMARK 500 2 DC A 2 0.07 SIDE CHAIN REMARK 500 2 DT B 10 0.07 SIDE CHAIN REMARK 500 2 DG B 11 0.08 SIDE CHAIN REMARK 500 2 DG B 13 0.06 SIDE CHAIN REMARK 500 2 DC C 14 0.08 SIDE CHAIN REMARK 500 2 DC C 16 0.09 SIDE CHAIN REMARK 500 2 DG C 18 0.08 SIDE CHAIN REMARK 500 2 DT C 19 0.07 SIDE CHAIN REMARK 500 2 DA C 20 0.07 SIDE CHAIN REMARK 500 2 DC C 21 0.06 SIDE CHAIN REMARK 500 2 DT C 22 0.09 SIDE CHAIN REMARK 500 2 DT C 23 0.10 SIDE CHAIN REMARK 500 2 DG C 25 0.05 SIDE CHAIN REMARK 500 2 DG C 26 0.06 SIDE CHAIN REMARK 500 3 DG A 6 0.07 SIDE CHAIN REMARK 500 3 DG B 11 0.05 SIDE CHAIN REMARK 500 3 DC C 14 0.06 SIDE CHAIN REMARK 500 3 DC C 15 0.07 SIDE CHAIN REMARK 500 3 DC C 16 0.10 SIDE CHAIN REMARK 500 3 DT C 23 0.08 SIDE CHAIN REMARK 500 3 DG C 25 0.07 SIDE CHAIN REMARK 500 4 DC A 1 0.09 SIDE CHAIN REMARK 500 4 DA A 5 0.06 SIDE CHAIN REMARK 500 4 DG B 11 0.07 SIDE CHAIN REMARK 500 4 DC C 14 0.09 SIDE CHAIN REMARK 500 4 DC C 16 0.10 SIDE CHAIN REMARK 500 4 DC C 21 0.07 SIDE CHAIN REMARK 500 4 DT C 23 0.13 SIDE CHAIN REMARK 500 5 DG A 6 0.05 SIDE CHAIN REMARK 500 5 DG B 11 0.07 SIDE CHAIN REMARK 500 5 DC C 14 0.11 SIDE CHAIN REMARK 500 5 DC C 16 0.10 SIDE CHAIN REMARK 500 5 DA C 20 0.06 SIDE CHAIN REMARK 500 5 DT C 22 0.06 SIDE CHAIN REMARK 500 5 DT C 23 0.10 SIDE CHAIN REMARK 500 5 DG C 25 0.06 SIDE CHAIN REMARK 500 6 DC A 1 0.10 SIDE CHAIN REMARK 500 6 DG A 6 0.05 SIDE CHAIN REMARK 500 6 DT B 10 0.06 SIDE CHAIN REMARK 500 6 DG B 11 0.08 SIDE CHAIN REMARK 500 6 DC C 14 0.09 SIDE CHAIN REMARK 500 6 DC C 16 0.10 SIDE CHAIN REMARK 500 6 DA C 20 0.06 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 84 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGA A 7 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1N0O RELATED DB: PDB REMARK 900 ENSEMBLE MODEL OF PDB ENTRY 1N0K REMARK 900 RELATED ID: 1N0K RELATED DB: PDB REMARK 900 MINIMIZED AVERAGE STRUCTURE OF PDB ENTRY 1N0O REMARK 900 RELATED ID: 1GJ1 RELATED DB: PDB REMARK 900 MINIMIZED AVERAGE STRUCTURE OF PDB ENTRY 1G5K DBREF 1G5K A 1 6 PDB 1G5K 1G5K 1 6 DBREF 1G5K B 8 13 PDB 1G5K 1G5K 8 13 DBREF 1G5K C 14 26 PDB 1G5K 1G5K 14 26 SEQRES 1 A 6 DC DC DA DA DA DG SEQRES 1 B 6 DA DC DT DG DG DG SEQRES 1 C 13 DC DC DC DA DG DT DA DC DT DT DT DG DG HET PGA A 7 10 HETNAM PGA 2-PHOSPHOGLYCOLIC ACID FORMUL 4 PGA C2 H5 O6 P LINK O3' DG A 6 P PGA A 7 1555 1555 1.58 SITE 1 AC1 1 DG A 6 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 MODEL 1