HEADER DNA 23-JAN-01 1HZ2 TITLE SOLUTION NMR STRUCTURE OF SELF-COMPLEMENTARY DUPLEX 5'-D(AGGCG*CCT)2 TITLE 2 CONTAINING A TRIMETHYLENE CROSSLINK AT THE N2 POSITION OF G*. MODEL TITLE 3 OF A MALONDIALDEHYDE CROSSLINK COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*AP*GP*GP*CP*GP*CP*CP*T)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DNA DUPLEX, INTERSTRAND CROSSLINK, DNA EXPDTA SOLUTION NMR AUTHOR P.A.DOOLEY,D.TSAROUHTSIS,G.A.KORBEL,L.V.NECHEV,J.SHEARER,I.S.ZEGAR, AUTHOR 2 C.M.HARRIS,M.P.STONE,T.M.HARRIS REVDAT 4 23-FEB-22 1HZ2 1 REMARK LINK REVDAT 3 24-FEB-09 1HZ2 1 VERSN REVDAT 2 01-AUG-01 1HZ2 1 JRNL REVDAT 1 07-FEB-01 1HZ2 0 JRNL AUTH P.A.DOOLEY,D.TSAROUHTSIS,G.A.KORBEL,L.V.NECHEV,J.SHEARER, JRNL AUTH 2 I.S.ZEGAR,C.M.HARRIS,M.P.STONE,T.M.HARRIS JRNL TITL STRUCTURAL STUDIES OF AN OLIGODEOXYNUCLEOTIDE CONTAINING A JRNL TITL 2 TRIMETHYLENE INTERSTRAND CROSS-LINK IN A 5'-(CPG) MOTIF: JRNL TITL 3 MODEL OF A MALONDIALDEHYDE CROSS-LINK. JRNL REF J.AM.CHEM.SOC. V. 123 1730 2001 JRNL REFN ISSN 0002-7863 JRNL PMID 11456774 JRNL DOI 10.1021/JA003163W REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX 95, X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER, A. T. (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FURTHER DETAILS ABOUT THE STRUCTURAL REMARK 3 REFINEMENT INCLUDING THE TRIMETHYLENE CHAIN CAN BE FOUND IN THE REMARK 3 JOURNAL ARTICLE REMARK 4 REMARK 4 1HZ2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JAN-01. REMARK 100 THE DEPOSITION ID IS D_1000012701. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303; 298 REMARK 210 PH : 7.1; 7.1 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 2 MM CROSSLINKED DUPLEX, 10 MM REMARK 210 SODIUM PHOSPHATE BUFFER, 0.1 M REMARK 210 NACL, 50 MM EDTA, PH 7.1; 2 MM REMARK 210 CROSSLINKED DUPLEX, 10 MM SODIUM REMARK 210 PHOSPHATE BUFFER, 0.1 M NACL, 50 REMARK 210 MM EDTA, PH 7.1 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; PE-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MARDIGRAS, X-PLOR 3.1, CPANEL, REMARK 210 SPHINX/LINSHA REMARK 210 METHOD USED : NOE-RESTRAINED MOLECULAR REMARK 210 DYNAMICS, SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL 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: 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 N2 DG A 5 H31 TME A 9 1.30 REMARK 500 H2'' DC B 14 O5' DC B 15 1.51 REMARK 500 H2'' DC A 6 O5' DC A 7 1.55 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 DA A 1 C8 DA A 1 N9 -0.107 REMARK 500 DG A 2 C8 DG A 2 N9 -0.064 REMARK 500 DC A 4 C4' DC A 4 C3' -0.080 REMARK 500 DC A 4 C3' DC A 4 C2' 0.100 REMARK 500 DC A 4 C2' DC A 4 C1' 0.068 REMARK 500 DG A 5 C8 DG A 5 N9 -0.048 REMARK 500 DG A 5 N9 DG A 5 C4 -0.050 REMARK 500 DC A 6 O4' DC A 6 C1' -0.086 REMARK 500 DC A 6 O4' DC A 6 C4' -0.129 REMARK 500 DC A 6 C1' DC A 6 N1 -0.114 REMARK 500 DC A 6 N1 DC A 6 C6 -0.100 REMARK 500 DC A 6 C5 DC A 6 C6 -0.106 REMARK 500 DC A 7 C3' DC A 7 C2' 0.077 REMARK 500 DT A 8 C5 DT A 8 C6 0.074 REMARK 500 DT A 8 C5 DT A 8 C7 0.075 REMARK 500 DA B 9 C8 DA B 9 N9 -0.107 REMARK 500 DG B 10 C8 DG B 10 N9 -0.064 REMARK 500 DC B 12 C4' DC B 12 C3' -0.080 REMARK 500 DC B 12 C3' DC B 12 C2' 0.102 REMARK 500 DC B 12 C2' DC B 12 C1' 0.064 REMARK 500 DG B 13 C8 DG B 13 N9 -0.046 REMARK 500 DC B 14 O4' DC B 14 C1' -0.086 REMARK 500 DC B 14 O4' DC B 14 C4' -0.130 REMARK 500 DC B 14 C1' DC B 14 N1 -0.115 REMARK 500 DC B 14 N1 DC B 14 C6 -0.105 REMARK 500 DC B 14 C5 DC B 14 C6 -0.106 REMARK 500 DC B 15 C3' DC B 15 C2' 0.085 REMARK 500 DT B 16 C5 DT B 16 C6 0.072 REMARK 500 DT B 16 C5 DT B 16 C7 0.069 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 DA A 1 C5 - N7 - C8 ANGL. DEV. = -3.8 DEGREES REMARK 500 DA A 1 N7 - C8 - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG A 2 C5 - N7 - C8 ANGL. DEV. = -3.4 DEGREES REMARK 500 DG A 2 N7 - C8 - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 DG A 3 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG A 3 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 DC A 4 O4' - C4' - C3' ANGL. DEV. = 4.3 DEGREES REMARK 500 DC A 4 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG A 5 O4' - C1' - N9 ANGL. DEV. = 11.2 DEGREES REMARK 500 DG A 5 C5 - N7 - C8 ANGL. DEV. = -3.5 DEGREES REMARK 500 DG A 5 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG A 5 N3 - C4 - N9 ANGL. DEV. = -3.6 DEGREES REMARK 500 DC A 6 C5' - C4' - O4' ANGL. DEV. = -12.6 DEGREES REMARK 500 DC A 6 C6 - N1 - C2 ANGL. DEV. = 5.3 DEGREES REMARK 500 DC A 6 C6 - N1 - C1' ANGL. DEV. = -12.1 DEGREES REMARK 500 DC A 6 C2 - N1 - C1' ANGL. DEV. = 6.7 DEGREES REMARK 500 DC A 6 C3' - O3' - P ANGL. DEV. = 10.6 DEGREES REMARK 500 DC A 7 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 DA B 9 C5 - N7 - C8 ANGL. DEV. = -3.8 DEGREES REMARK 500 DA B 9 N7 - C8 - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 DG B 10 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG B 10 C5 - N7 - C8 ANGL. DEV. = -3.3 DEGREES REMARK 500 DG B 10 N7 - C8 - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 DG B 11 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG B 11 C8 - N9 - C4 ANGL. DEV. = -3.4 DEGREES REMARK 500 DC B 12 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 DC B 12 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 12.6 DEGREES REMARK 500 DG B 13 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 DC B 14 C5' - C4' - O4' ANGL. DEV. = -12.2 DEGREES REMARK 500 DC B 14 C6 - N1 - C2 ANGL. DEV. = 5.2 DEGREES REMARK 500 DC B 14 N3 - C4 - C5 ANGL. DEV. = -2.5 DEGREES REMARK 500 DC B 14 C6 - N1 - C1' ANGL. DEV. = -11.8 DEGREES REMARK 500 DC B 14 C3' - O3' - P ANGL. DEV. = 10.7 DEGREES REMARK 500 DC B 15 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DT B 16 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT B 16 C5 - C6 - N1 ANGL. DEV. = -3.8 DEGREES 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 DG A 3 0.05 SIDE CHAIN REMARK 500 DG B 11 0.05 SIDE CHAIN 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 TME A 9 DBREF 1HZ2 A 1 8 PDB 1HZ2 1HZ2 1 8 DBREF 1HZ2 B 9 16 PDB 1HZ2 1HZ2 9 16 SEQRES 1 A 8 DA DG DG DC DG DC DC DT SEQRES 1 B 8 DA DG DG DC DG DC DC DT HET TME A 9 9 HETNAM TME PROPANE FORMUL 3 TME C3 H8 LINK N2 DG A 5 C3 TME A 9 1555 1555 1.46 LINK C1 TME A 9 N2 DG B 13 1555 1555 1.47 SITE 1 AC1 4 DG A 5 DC A 6 DG B 13 DC B 14 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