HEADER DNA 24-MAR-04 1SSJ TITLE A DNA DUPLEX CONTAINING A CHOLESTEROL ADDUCT (BETA-ANOMER) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*AP*CP*(HOB)P*GP*GP*AP*AP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(GP*TP*TP*CP*CP*GP*GP*TP*GP*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 DOUBLE HELIX, MODIFIED DNA, CHOLESTEROL ADDUCT, DNA LESION, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR I.GOMEZ-PINTO,E.CUBERO,S.G.KALKO,V.MONACO,G.VAN DER MAREL,J.H.VAN AUTHOR 2 BOOM,M.OROZCO,C.GONZALEZ REVDAT 4 13-JUL-11 1SSJ 1 VERSN REVDAT 3 24-FEB-09 1SSJ 1 VERSN REVDAT 2 08-JUN-04 1SSJ 1 JRNL REVDAT 1 01-JUN-04 1SSJ 0 JRNL AUTH I.GOMEZ-PINTO,E.CUBERO,S.G.KALKO,V.MONACO,G.VAN DER MAREL, JRNL AUTH 2 J.H.VAN BOOM,M.OROZCO,C.GONZALEZ JRNL TITL EFFECT OF BULKY LESIONS ON DNA: SOLUTION STRUCTURE OF A DNA JRNL TITL 2 DUPLEX CONTAINING A CHOLESTEROL ADDUCT. JRNL REF J.BIOL.CHEM. V. 279 24552 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 15047709 JRNL DOI 10.1074/JBC.M311751200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 5.0 REMARK 3 AUTHORS : KOLLMAN P., ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 380 NOE-DERIVED DISTANCE CONSTRAINTS OBTAINED FROM A COMPLETE REMARK 3 RELAXATION MATRIX REFINEMENT. THE STRUCTURES WERE CALCULATED BY REMARK 3 USING RESTRAINED MOLECULAR DYNAMICS WITH EXPLICIT SOLVENT, AND REMARK 3 APPLYING THE PARTICLE MESH EWALD METHOD REMARK 4 REMARK 4 1SSJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAR-04. REMARK 100 THE RCSB ID CODE IS RCSB021966. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 100 MM NACL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2MM DUPLEX, 100MM NACL, 90% H2O, REMARK 210 10% D2O OR 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DYANA 5.1, MARDIGRAS 5.2, REMARK 210 XWINNMR 1.3, XEASY 1.0 REMARK 210 METHOD USED : RELAXATION MATRIX RESTRAINED REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 3 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 DA A 9 C5' DA A 9 C4' 0.044 REMARK 500 4 DC A 4 C4 DC A 4 N4 -0.056 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 1 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DC A 1 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DC A 2 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DA A 3 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA A 3 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DA A 3 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DC A 4 O4' - C1' - N1 ANGL. DEV. = 7.8 DEGREES REMARK 500 1 DC A 4 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DA A 8 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA A 8 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DA A 8 N1 - C6 - N6 ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DA A 9 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DA A 9 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA A 9 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 9 N1 - C6 - N6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DC A 10 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG B 11 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 1 DT B 12 O4' - C4' - C3' ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DT B 12 C6 - C5 - C7 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DT B 13 C6 - C5 - C7 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DC B 14 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DG B 16 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG B 17 C4' - C3' - C2' ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DT B 18 O4' - C1' - C2' ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DT B 18 C6 - C5 - C7 ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DG B 19 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DC A 1 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 2 DC A 2 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 2 DA A 3 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DA A 3 N1 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 2 DC A 2 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 2 DC A 4 O4' - C1' - N1 ANGL. DEV. = 6.7 DEGREES REMARK 500 2 DC A 4 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DA A 8 C4 - C5 - C6 ANGL. DEV. = -4.2 DEGREES REMARK 500 2 DA A 8 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DA A 8 N1 - C6 - N6 ANGL. DEV. = -6.6 DEGREES REMARK 500 2 DA A 9 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 2 DA A 9 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DA A 9 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 DC A 10 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 2 DG B 11 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DG B 11 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DT B 12 O4' - C4' - C3' ANGL. DEV. = 4.9 DEGREES REMARK 500 2 DT B 12 C6 - C5 - C7 ANGL. DEV. = -5.6 DEGREES REMARK 500 2 DT B 13 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 2 DC B 14 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 DC B 15 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 269 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 DC A 4 0.10 SIDE CHAIN REMARK 500 1 DG A 6 0.11 SIDE CHAIN REMARK 500 1 DG B 11 0.06 SIDE CHAIN REMARK 500 1 DT B 13 0.06 SIDE CHAIN REMARK 500 1 DC B 14 0.08 SIDE CHAIN REMARK 500 1 DG B 17 0.08 SIDE CHAIN REMARK 500 1 DG B 19 0.11 SIDE CHAIN REMARK 500 2 DC A 4 0.09 SIDE CHAIN REMARK 500 2 DG A 6 0.11 SIDE CHAIN REMARK 500 2 DG A 7 0.11 SIDE CHAIN REMARK 500 2 DA A 8 0.06 SIDE CHAIN REMARK 500 2 DG B 11 0.06 SIDE CHAIN REMARK 500 2 DG B 16 0.06 SIDE CHAIN REMARK 500 2 DG B 19 0.07 SIDE CHAIN REMARK 500 3 DC A 4 0.12 SIDE CHAIN REMARK 500 3 DG A 6 0.12 SIDE CHAIN REMARK 500 3 DT B 13 0.06 SIDE CHAIN REMARK 500 3 DC B 14 0.07 SIDE CHAIN REMARK 500 3 DG B 17 0.06 SIDE CHAIN REMARK 500 3 DG B 19 0.06 SIDE CHAIN REMARK 500 4 DA A 3 0.07 SIDE CHAIN REMARK 500 4 DC A 4 0.08 SIDE CHAIN REMARK 500 4 DG A 6 0.10 SIDE CHAIN REMARK 500 4 DA A 9 0.07 SIDE CHAIN REMARK 500 4 DC B 14 0.09 SIDE CHAIN REMARK 500 4 DC B 15 0.08 SIDE CHAIN REMARK 500 4 DG B 16 0.07 SIDE CHAIN REMARK 500 4 DG B 19 0.09 SIDE CHAIN REMARK 500 5 DA A 3 0.07 SIDE CHAIN REMARK 500 5 DC A 4 0.07 SIDE CHAIN REMARK 500 5 DG A 6 0.12 SIDE CHAIN REMARK 500 5 DG A 7 0.09 SIDE CHAIN REMARK 500 5 DT B 13 0.10 SIDE CHAIN REMARK 500 5 DG B 19 0.06 SIDE CHAIN REMARK 500 6 DC A 4 0.10 SIDE CHAIN REMARK 500 6 DG A 6 0.11 SIDE CHAIN REMARK 500 6 DG A 7 0.10 SIDE CHAIN REMARK 500 6 DT B 13 0.08 SIDE CHAIN REMARK 500 6 DC B 14 0.07 SIDE CHAIN REMARK 500 6 DG B 19 0.07 SIDE CHAIN REMARK 500 7 DC A 4 0.10 SIDE CHAIN REMARK 500 7 DG A 6 0.07 SIDE CHAIN REMARK 500 7 DA A 8 0.06 SIDE CHAIN REMARK 500 7 DA A 9 0.07 SIDE CHAIN REMARK 500 7 DT B 13 0.09 SIDE CHAIN REMARK 500 7 DG B 16 0.09 SIDE CHAIN REMARK 500 7 DG B 19 0.07 SIDE CHAIN REMARK 500 8 DC A 4 0.09 SIDE CHAIN REMARK 500 8 DG A 6 0.07 SIDE CHAIN REMARK 500 8 DG A 7 0.12 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 72 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SP6 RELATED DB: PDB REMARK 900 A DNA DUPLEX CONTAINING A CHOLESTEROL ADDUCT (ALPHA-ANOMER) DBREF 1SSJ A 1 10 PDB 1SSJ 1SSJ 1 10 DBREF 1SSJ B 11 20 PDB 1SSJ 1SSJ 11 20 SEQRES 1 A 10 DC DC DA DC HOB DG DG DA DA DC SEQRES 1 B 10 DG DT DT DC DC DG DG DT DG DG HET HOB A 5 105 HETNAM HOB BETA-CHOLEST-5-EN-3-YL 3-[(2-DEOXY-5-O-PHOSPHONO-ALPHA- HETNAM 2 HOB D-GLYCERO-PENTOFURANOSYL)OXY]PROPYLCARBAMATE FORMUL 1 HOB C36 H62 N O8 P LINK O3' DC A 4 P HOB A 5 1555 1555 1.60 LINK O3' HOB A 5 P DG A 6 1555 1555 1.60 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 232 0 1 0 0 0 0 6 0 0 0 2 END