PDB Short entry for 2L2U HEADER DNA 27-AUG-10 2L2U TITLE NMR SOLUTION STRUCTURES OF +3 (5' STAGGERED) BISTRANDED ABASIC SITE TITLE 2 LESIONS IN DNA CAVEAT 2L2U CHIRALITY ERROR AT ATOM C4' OF DT8 IN MODEL 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*AP*GP*CP*GP*(3DR)P*GP*TP*AP*TP*AP*AP*GP*C)- COMPND 3 3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*GP*CP*TP*TP*AP*(3DR)P*AP*CP*AP*CP*GP*CP*TP*G)- COMPND 8 3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHETIC PEPTIDE; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: SYNTHETIC PEPTIDE KEYWDS ABASIC LESION, BISTRANDED DNA LESIONS, CLUSTERED DNA DAMAGE, MULTIPLE KEYWDS 2 DNA DAMAGE, IONIZING RADIATION, DNA EXPDTA SOLUTION NMR NUMMDL 4 AUTHOR R.D.HAZEL,C.DE LOS SANTOS REVDAT 2 01-MAY-24 2L2U 1 LINK REVDAT 1 03-NOV-10 2L2U 0 JRNL AUTH R.D.HAZEL,C.DE LOS SANTOS JRNL TITL NMR SOLUTION STRUCTURES OF CLUSTERED ABASIC SITE LESIONS IN JRNL TITL 2 DNA: STRUCTURAL DIFFERENCES BETWEEN 3'-STAGGERED (-3) AND JRNL TITL 3 5'-STAGGERED (+3) BISTRANDED LESIONS. JRNL REF BIOCHEMISTRY V. 49 8978 2010 JRNL REFN ISSN 0006-2960 JRNL PMID 20825249 JRNL DOI 10.1021/BI101021E REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1, X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER (X-PLOR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: AUTHORS INDICATE CHIRALITY ERROR AT DT8 REMARK 3 IN MODEL 1 DUE TO FLEXIBILITY OF THE DNA DUPLEX IN SOLUTION REMARK 4 REMARK 4 2L2U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000101886. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : UNKNOWN MM DNA (5' REMARK 210 -D(*CP*AP*GP*CP*GP*(3DR)P*GP*TP*AP*TP*AP*AP*GP*C)-3'), UNKNOWN REMARK 210 MM DNA (5'-D(*GP*CP*TP*TP*AP*(3DR)P*AP*CP*AP*CP*GP*CP*TP*G)-3'), REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H COSY; REMARK 210 2D DQF-COSY; 2D 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 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 : MOLECULAR DYNAMICS, DGSA REMARK 210 -DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 4 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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 1 DC A 1 C4 DC A 1 N4 0.097 REMARK 500 1 DA A 2 C6 DA A 2 N6 0.096 REMARK 500 1 DG A 3 C2 DG A 3 N2 0.087 REMARK 500 1 DC A 4 C4 DC A 4 N4 0.096 REMARK 500 1 DG A 5 C2 DG A 5 N2 0.084 REMARK 500 1 DG A 7 C2 DG A 7 N2 0.087 REMARK 500 1 DT A 8 C5 DT A 8 C7 0.037 REMARK 500 1 DA A 9 C6 DA A 9 N6 0.095 REMARK 500 1 DA A 11 C6 DA A 11 N6 0.099 REMARK 500 1 DA A 12 C6 DA A 12 N6 0.095 REMARK 500 1 DG A 13 C2 DG A 13 N2 0.085 REMARK 500 1 DC A 14 C4 DC A 14 N4 0.094 REMARK 500 1 DG B 15 C2 DG B 15 N2 0.086 REMARK 500 1 DC B 16 C4 DC B 16 N4 0.095 REMARK 500 1 DA B 19 C6 DA B 19 N6 0.096 REMARK 500 1 DA B 21 C6 DA B 21 N6 0.090 REMARK 500 1 DC B 22 C4 DC B 22 N4 0.095 REMARK 500 1 DA B 23 C6 DA B 23 N6 0.096 REMARK 500 1 DC B 24 C4 DC B 24 N4 0.093 REMARK 500 1 DG B 25 C2 DG B 25 N2 0.086 REMARK 500 1 DC B 26 C4 DC B 26 N4 0.096 REMARK 500 1 DG B 28 C2 DG B 28 N2 0.088 REMARK 500 2 DC A 1 C4 DC A 1 N4 0.098 REMARK 500 2 DA A 2 C6 DA A 2 N6 0.094 REMARK 500 2 DG A 3 C2 DG A 3 N2 0.087 REMARK 500 2 DC A 4 C4 DC A 4 N4 0.096 REMARK 500 2 DG A 5 C2 DG A 5 N2 0.085 REMARK 500 2 DG A 7 C2 DG A 7 N2 0.086 REMARK 500 2 DT A 8 C5 DT A 8 C7 0.038 REMARK 500 2 DA A 9 C6 DA A 9 N6 0.092 REMARK 500 2 DA A 11 C6 DA A 11 N6 0.099 REMARK 500 2 DA A 12 C6 DA A 12 N6 0.094 REMARK 500 2 DG A 13 C2 DG A 13 N2 0.086 REMARK 500 2 DC A 14 C4 DC A 14 N4 0.094 REMARK 500 2 DG B 15 C2 DG B 15 N2 0.085 REMARK 500 2 DC B 16 C4 DC B 16 N4 0.095 REMARK 500 2 DA B 19 C6 DA B 19 N6 0.096 REMARK 500 2 DA B 21 C6 DA B 21 N6 0.094 REMARK 500 2 DC B 22 C4 DC B 22 N4 0.092 REMARK 500 2 DA B 23 C6 DA B 23 N6 0.097 REMARK 500 2 DC B 24 C4 DC B 24 N4 0.092 REMARK 500 2 DG B 25 C2 DG B 25 N2 0.084 REMARK 500 2 DC B 26 C4 DC B 26 N4 0.096 REMARK 500 2 DG B 28 C2 DG B 28 N2 0.089 REMARK 500 3 DC A 1 C4 DC A 1 N4 0.097 REMARK 500 3 DA A 2 C6 DA A 2 N6 0.094 REMARK 500 3 DG A 3 C2 DG A 3 N2 0.087 REMARK 500 3 DC A 4 C4 DC A 4 N4 0.098 REMARK 500 3 DG A 5 C2 DG A 5 N2 0.085 REMARK 500 3 DG A 7 C2 DG A 7 N2 0.084 REMARK 500 REMARK 500 THIS ENTRY HAS 86 BOND DEVIATIONS. 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 DA A 2 C5' - C4' - O4' ANGL. DEV. = 8.1 DEGREES REMARK 500 1 DG A 3 C5' - C4' - O4' ANGL. DEV. = 8.3 DEGREES REMARK 500 1 DC A 4 C5' - C4' - O4' ANGL. DEV. = 7.8 DEGREES REMARK 500 1 DG A 5 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 7 C5' - C4' - O4' ANGL. DEV. = 9.2 DEGREES REMARK 500 1 DG A 7 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 7 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG A 7 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DT A 8 C5' - C4' - O4' ANGL. DEV. = 6.8 DEGREES REMARK 500 1 DA A 12 C5' - C4' - O4' ANGL. DEV. = 7.3 DEGREES REMARK 500 1 DG B 15 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG B 15 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 1 DT B 17 O4' - C4' - C3' ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DT B 17 O4' - C1' - C2' ANGL. DEV. = -6.5 DEGREES REMARK 500 1 DT B 17 C4 - C5 - C6 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DT B 17 C4 - C5 - C7 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DT B 17 C6 - C5 - C7 ANGL. DEV. = -8.5 DEGREES REMARK 500 1 DT B 18 C5' - C4' - O4' ANGL. DEV. = 10.7 DEGREES REMARK 500 1 DT B 18 C4 - C5 - C7 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 DT B 18 C6 - C5 - C7 ANGL. DEV. = -8.7 DEGREES REMARK 500 1 DA B 21 C5' - C4' - O4' ANGL. DEV. = 8.6 DEGREES REMARK 500 1 DA B 21 O4' - C1' - C2' ANGL. DEV. = -7.2 DEGREES REMARK 500 1 DA B 23 C5' - C4' - O4' ANGL. DEV. = 6.9 DEGREES REMARK 500 1 DA B 23 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DT B 27 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DA A 2 C5' - C4' - O4' ANGL. DEV. = 8.3 DEGREES REMARK 500 2 DG A 3 C5' - C4' - O4' ANGL. DEV. = 7.6 DEGREES REMARK 500 2 DG A 3 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DC A 4 C5' - C4' - O4' ANGL. DEV. = 6.8 DEGREES REMARK 500 2 DG A 5 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 3DR A 6 C3' - O3' - P ANGL. DEV. = 9.0 DEGREES REMARK 500 2 DG A 7 C5' - C4' - O4' ANGL. DEV. = 8.3 DEGREES REMARK 500 2 DG A 7 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DG A 7 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DG A 7 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 DA A 12 C5' - C4' - O4' ANGL. DEV. = 7.0 DEGREES REMARK 500 2 DG A 13 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DG B 15 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DG B 15 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 DT B 17 O4' - C4' - C3' ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DT B 17 O4' - C1' - C2' ANGL. DEV. = -5.8 DEGREES REMARK 500 2 DT B 17 C4 - C5 - C6 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DT B 17 C4 - C5 - C7 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DT B 17 C6 - C5 - C7 ANGL. DEV. = -7.8 DEGREES REMARK 500 2 DT B 18 C5' - C4' - O4' ANGL. DEV. = 10.7 DEGREES REMARK 500 2 DT B 18 C4 - C5 - C7 ANGL. DEV. = 6.0 DEGREES REMARK 500 2 DT B 18 C6 - C5 - C7 ANGL. DEV. = -8.6 DEGREES REMARK 500 2 DA B 19 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 109 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YCW RELATED DB: PDB REMARK 900 RELATED ID: 1YCT RELATED DB: PDB DBREF 2L2U A 1 14 PDB 2L2U 2L2U 1 14 DBREF 2L2U B 15 28 PDB 2L2U 2L2U 15 28 SEQRES 1 A 14 DC DA DG DC DG 3DR DG DT DA DT DA DA DG SEQRES 2 A 14 DC SEQRES 1 B 14 DG DC DT DT DA 3DR DA DC DA DC DG DC DT SEQRES 2 B 14 DG HET 3DR A 6 19 HET 3DR B 20 19 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETSYN 3DR ABASIC DIDEOXYRIBOSE FORMUL 1 3DR 2(C5 H11 O6 P) LINK O3' DG A 5 P 3DR A 6 1555 1555 1.62 LINK O3' 3DR A 6 P DG A 7 1555 1555 1.62 LINK O3' DA B 19 P 3DR B 20 1555 1555 1.62 LINK O3' 3DR B 20 P DA B 21 1555 1555 1.62 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