PDB Short entry for 1A9G HEADER DNA 06-APR-98 1A9G TITLE APURINIC DNA WITH BOUND WATER AT THE DAMAGED SITE AND N3 OF CYTOSINE, TITLE 2 BETA FORM, NMR, 1 STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*GP*AP*AABP*AP*CP*GP*CP*C)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*GP*GP*CP*GP*TP*CP*TP*CP*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 DAMAGED DNA, APURINIC DNA, WATER, DNA EXPDTA SOLUTION NMR AUTHOR R.D.BEGER,P.H.BOLTON REVDAT 4 10-APR-24 1A9G 1 LINK REVDAT 3 09-JUL-14 1A9G 1 HETNAM VERSN REVDAT 2 24-FEB-09 1A9G 1 VERSN REVDAT 1 15-JUL-98 1A9G 0 JRNL AUTH R.D.BEGER,P.H.BOLTON JRNL TITL STRUCTURES OF APURINIC AND APYRIMIDINIC SITES IN DUPLEX JRNL TITL 2 DNAS. JRNL REF J.BIOL.CHEM. V. 273 15565 1998 JRNL REFN ISSN 0021-9258 JRNL PMID 9624147 JRNL DOI 10.1074/JBC.273.25.15565 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1A9G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170558. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 50 MM KCL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : TRIS REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; PECOSY; TOCSY; ROESY; REMARK 210 QUIET-NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 400 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : UNITY; INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR REMARK 210 METHOD USED : MATRIX RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : AVERAGE OF 5 STRUCTURES THAT THE REMARK 210 NOESY BACK CALCULATION AGREES REMARK 210 WITH EXPERIMENTAL NOESY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: 100MS NOESY, 250MS NOESY 250MS QUIETNOESY 70MS BAND REMARK 210 -SELECTIVE J TOCSY FOR PHOSPHOROUS "J SCALE" SET TO 2 AND 3 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HO1' AAB A 6 H1 HOH B 23 1.28 REMARK 500 REMARK 500 REMARK: NULL 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 DC A 1 O5' DC A 1 C5' -0.183 REMARK 500 DC A 1 C5' DC A 1 C4' -0.229 REMARK 500 DC A 1 C4' DC A 1 C3' -0.163 REMARK 500 DC A 1 C3' DC A 1 C2' -0.063 REMARK 500 DC A 1 C2' DC A 1 C1' -0.176 REMARK 500 DC A 1 O4' DC A 1 C1' -0.081 REMARK 500 DC A 1 O4' DC A 1 C4' -0.118 REMARK 500 DC A 1 O3' DC A 1 C3' -0.126 REMARK 500 DC A 1 C2 DC A 1 O2 -0.126 REMARK 500 DC A 1 C4 DC A 1 N4 -0.089 REMARK 500 DC A 1 N1 DC A 1 C2 -0.173 REMARK 500 DC A 1 N1 DC A 1 C6 -0.120 REMARK 500 DC A 1 C2 DC A 1 N3 -0.076 REMARK 500 DC A 1 N3 DC A 1 C4 -0.123 REMARK 500 DC A 1 C4 DC A 1 C5 -0.165 REMARK 500 DC A 1 C5 DC A 1 C6 -0.075 REMARK 500 DC A 1 O3' DG A 2 P -0.201 REMARK 500 DG A 2 P DG A 2 OP1 -0.140 REMARK 500 DG A 2 P DG A 2 OP2 -0.115 REMARK 500 DG A 2 P DG A 2 O5' -0.162 REMARK 500 DG A 2 C4 DG A 2 C5 -0.043 REMARK 500 DG A 2 C6 DG A 2 N1 -0.048 REMARK 500 DG A 2 N7 DG A 2 C8 -0.039 REMARK 500 DG A 2 N9 DG A 2 C4 -0.053 REMARK 500 DC A 3 P DC A 3 OP1 -0.135 REMARK 500 DC A 3 P DC A 3 OP2 -0.188 REMARK 500 DC A 3 P DC A 3 O5' -0.161 REMARK 500 DC A 3 C5' DC A 3 C4' -0.139 REMARK 500 DC A 3 C4' DC A 3 C3' -0.068 REMARK 500 DC A 3 C3' DC A 3 C2' -0.049 REMARK 500 DC A 3 O4' DC A 3 C4' -0.077 REMARK 500 DC A 3 O3' DC A 3 C3' -0.049 REMARK 500 DA A 5 P DA A 5 O5' -0.066 REMARK 500 DA A 7 P DA A 7 OP1 -0.130 REMARK 500 DA A 7 P DA A 7 O5' -0.080 REMARK 500 DC A 8 P DC A 8 OP2 -0.107 REMARK 500 DC A 8 O3' DC A 8 C3' -0.041 REMARK 500 DC A 10 P DC A 10 OP2 -0.111 REMARK 500 DC A 10 P DC A 10 O5' -0.066 REMARK 500 DC A 10 C3' DC A 10 C2' -0.061 REMARK 500 DC A 10 O4' DC A 10 C4' -0.067 REMARK 500 DC A 11 C3' DC A 11 C2' -0.061 REMARK 500 DC A 11 C4 DC A 11 N4 -0.074 REMARK 500 DC A 11 N1 DC A 11 C2 -0.087 REMARK 500 DC A 11 C2 DC A 11 N3 -0.064 REMARK 500 DC A 11 C4 DC A 11 C5 -0.073 REMARK 500 DC A 11 C5 DC A 11 C6 -0.051 REMARK 500 DG B 12 C5' DG B 12 C4' -0.123 REMARK 500 DG B 12 C4' DG B 12 C3' -0.118 REMARK 500 DG B 12 C3' DG B 12 C2' -0.050 REMARK 500 REMARK 500 THIS ENTRY HAS 116 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 DC A 1 C4' - C3' - C2' ANGL. DEV. = -4.2 DEGREES REMARK 500 DC A 1 O4' - C1' - N1 ANGL. DEV. = 6.3 DEGREES REMARK 500 DC A 1 C6 - N1 - C2 ANGL. DEV. = -3.2 DEGREES REMARK 500 DC A 1 C2 - N3 - C4 ANGL. DEV. = 4.1 DEGREES REMARK 500 DC A 1 N3 - C4 - C5 ANGL. DEV. = -3.9 DEGREES REMARK 500 DC A 1 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG A 2 C3' - O3' - P ANGL. DEV. = 8.0 DEGREES REMARK 500 DC A 3 O4' - C4' - C3' ANGL. DEV. = 5.3 DEGREES REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA A 7 C4' - C3' - C2' ANGL. DEV. = -4.4 DEGREES REMARK 500 DA A 7 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 DC A 8 O4' - C1' - C2' ANGL. DEV. = -7.5 DEGREES REMARK 500 DC A 8 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 DG A 9 C3' - O3' - P ANGL. DEV. = 9.2 DEGREES REMARK 500 DC A 10 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC A 10 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC A 10 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES REMARK 500 DC A 11 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 DC A 11 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG B 12 C4' - C3' - C2' ANGL. DEV. = -4.4 DEGREES REMARK 500 DG B 12 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 DG B 13 N9 - C4 - C5 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC B 14 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC B 14 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 DC B 14 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 DG B 15 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 DC B 17 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT B 18 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DT B 18 C3' - O3' - P ANGL. DEV. = 10.3 DEGREES REMARK 500 DC B 19 C3' - O3' - P ANGL. DEV. = 9.1 DEGREES REMARK 500 DG B 20 C3' - O3' - P ANGL. DEV. = 10.3 DEGREES REMARK 500 DC B 21 C3' - O3' - P ANGL. DEV. = 9.1 DEGREES REMARK 500 DG B 22 C3' - C2' - C1' ANGL. DEV. = 18.0 DEGREES REMARK 500 DG B 22 O4' - C1' - C2' ANGL. DEV. = -5.7 DEGREES REMARK 500 DG B 22 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 DG B 22 C2 - N3 - C4 ANGL. DEV. = 4.8 DEGREES REMARK 500 DG B 22 C5 - C6 - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 DG B 22 C5 - N7 - C8 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG B 22 N7 - C8 - N9 ANGL. DEV. = -4.2 DEGREES REMARK 500 DG B 22 C8 - N9 - C4 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG B 22 C6 - C5 - N7 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG B 22 N1 - C6 - O6 ANGL. DEV. = -5.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 1A9G A 1 11 PDB 1A9G 1A9G 1 11 DBREF 1A9G B 12 22 PDB 1A9G 1A9G 12 22 SEQRES 1 A 11 DC DG DC DG DA AAB DA DC DG DC DC SEQRES 1 B 11 DG DG DC DG DT DC DT DC DG DC DG HET AAB A 6 20 HETNAM AAB 2'-DEOXY-RIBOFURANOSE-5'-MONOPHOSPHATE HETSYN AAB ABASIC DEOXYRIBOSE FORMUL 1 AAB C5 H11 O7 P FORMUL 3 HOH *(H2 O) LINK O3' DA A 5 P AAB A 6 1555 1555 1.54 LINK O3' AAB A 6 P DA A 7 1555 1555 1.57 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