Header list of 2hli.pdb file
Complete list - 31 201 Bytes
HEADER DNA 07-JUL-06 2HLI TITLE SOLUTION STRUCTURE OF CROTONALDEHYDE-DERIVED N2-[3-OXO-1(S)-METHYL- TITLE 2 PROPYL]-DG DNA ADDUCT IN THE 5'-CPG-3' SEQUENCE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA DODECAMER WITH S-CROTONALDEHYDE ADDUCT; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA DODECAMER; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: ALL ADDUCTED SEQUENCES WERE MADE BY DR. RIZZO AND DR. SOURCE 4 HARRIS LAB AT VANDERBILT; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES KEYWDS INTERSTRAND DNA CROSS-LINK; S-CROTONALDEHYDE-DG ADDUCT; 5'-CPG-3' KEYWDS 2 SEQUENCE, DNA EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR Y.-J.CHO,H.WANG,I.D.KOZEKOV,A.J.KURTZ,J.JACOB,M.VOEHLER,J.SMITH, AUTHOR 2 T.M.HARRIS,C.J.RIZZO,M.P.STONE REVDAT 3 31-JAN-18 2HLI 1 AUTHOR REMARK REVDAT 2 24-FEB-09 2HLI 1 VERSN REVDAT 1 19-SEP-06 2HLI 0 JRNL AUTH Y.-J.CHO,H.WANG,I.D.KOZEKOV,A.KOZEKOVA,A.J.KURTZ,J.JACOB, JRNL AUTH 2 M.VOEHLER,J.SMITH,T.M.HARRIS,C.J.RIZZO,R.S.LLOYD,M.P.STONE JRNL TITL ORIENTATION OF THE CROTONALDEHYDE-DERIVED JRNL TITL 2 N(2)-[3-OXO-1(S)-METHYL-PROPYL]-DG DNA ADDUCT HINDERS JRNL TITL 3 INTERSTRAND CROSS-LINK FORMATION IN THE 5'-CPG-3' SEQUENCE JRNL REF CHEM.RES.TOXICOL. V. 19 1019 2006 JRNL REFN ISSN 0893-228X JRNL PMID 16918240 JRNL DOI 10.1021/TX0600604 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, AMBER 8.0 REMARK 3 AUTHORS : BRUKER (XWINNMR), CASE ET AL (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 308 DISTANCE RESTRAINTS, 90 SUGAR REMARK 3 PUCKER RESTRAINTS, 52 H-BONDING RESTRAINTS REMARK 4 REMARK 4 2HLI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUL-06. REMARK 100 THE DEPOSITION ID IS D_1000038483. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 9.3 REMARK 210 IONIC STRENGTH : 0.1 M NACL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM IN 0.25 ML; 10 MM SODIUM REMARK 210 PHOSPHATE BUFFER; 0.1 M NACL; 50 REMARK 210 UMNA2EDTA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; E-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.3, FELIX 2000, REMARK 210 MARDIGRAS 5.2.1, CORMA 5.2 REMARK 210 METHOD USED : DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING MOLECULAR DYNAMICS REMARK 210 MATRIX RELAXATION AND TORSION REMARK 210 ANGLE REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 10 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. 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 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 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC A 2 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DT A 3 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DT A 3 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 DC A 6 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC A 6 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 DA A 8 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DA A 8 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 DA A 8 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA A 8 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT A 10 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC A 11 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 DC A 12 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC A 12 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG B 14 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA B 15 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA B 15 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 DA B 15 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA B 15 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 DC B 16 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 DC B 16 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC B 16 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 DT B 17 O4' - C1' - N1 ANGL. DEV. = 6.9 DEGREES REMARK 500 DT B 17 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 DC B 18 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC B 18 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 DG B 19 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC B 20 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC B 20 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 DT B 21 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA B 22 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA B 22 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 DA B 22 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA B 22 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 DG B 23 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC B 24 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC B 24 N3 - C2 - O2 ANGL. DEV. = -5.0 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 DC A 2 0.07 SIDE CHAIN REMARK 500 DT A 3 0.06 SIDE CHAIN REMARK 500 DG B 14 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2HLI A 1 12 PDB 2HLI 2HLI 1 12 DBREF 2HLI B 13 24 PDB 2HLI 2HLI 13 24 SEQRES 1 A 12 DG DC DT DA DG DC KAG DA DG DT DC DC SEQRES 1 B 12 DG DG DA DC DT DC DG DC DT DA DG DC MODRES 2HLI KAG A 7 G HET KAG A 7 44 HETNAM KAG 2'-DEOXY-N-[(1S)-1-METHYL-3-OXOPROPYL]GUANOSINE 5'- HETNAM 2 KAG PHOSPHATE FORMUL 1 KAG C14 H20 N5 O8 P LINK O3' DC A 6 P KAG A 7 1555 1555 1.61 LINK O3' KAG A 7 P DA A 8 1555 1555 1.61 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
Complete list - 31 201 Bytes