10 20 30 40 50 60 70 80 1GJ0 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 31-OCT-00 1GJ0
TITLE NMR STRUCTURE OF AN OLIGONUCLEOTIDE CONTAINING AN ABASIC TITLE 2 SITE: BETA ANOMER
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*AP*AP*AP*GP*(AAB)P*AP*CP*TP*GP*GP*G)- COMPND 3 3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*CP*CP*CP*AP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3'; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES
KEYWDS DAMAGED DNA, APYRIMIDINIC SITE
EXPDTA SOLUTION NMR
AUTHOR S.T.HOEHN,C.J.TURNER,J.STUBBE
REVDAT 2 24-FEB-09 1GJ0 1 VERSN REVDAT 1 22-AUG-01 1GJ0 0
JRNL AUTH S.T.HOEHN,C.J.TURNER,J.STUBBE JRNL TITL SOLUTION STRUCTURE OF AN OLIGONUCLEOTIDE JRNL TITL 2 CONTAINING AN ABASIC SITE: EVIDENCE FOR AN UNUSUAL JRNL TITL 3 DEOXYRIBOSE CONFORMATION. JRNL REF NUCLEIC ACIDS RES. V. 29 3413 2001 JRNL REFN ISSN 0305-1048 JRNL PMID 11504879 JRNL DOI 10.1093/NAR/29.16.3413
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON 475 NOE- REMARK 3 DERIVED DISTANCE CONSTRAINTS AND 101 DIHEDRAL ANGLE RESTRAINTS.
REMARK 4 REMARK 4 1GJ0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-NOV-00. REMARK 100 THE RCSB ID CODE IS RCSB001566.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293; 278; 298 REMARK 210 PH : 6.8; 6.8; 6.8 REMARK 210 IONIC STRENGTH : 10 MM SODIUM PHOSPHATE REMARK 210 BUFFER; 10 MM SODIUM PHOSPHATE REMARK 210 BUFFER; 10 MM SODIUM PHOSPHATE REMARK 210 BUFFER REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 2.5 MM ABASIC SITE CONTAINING REMARK 210 DUPLEX OLIGONUCLEOTIDE; 10 MM REMARK 210 SODIUM PHOSPHATE BUFFER; 2.5 REMARK 210 MM ABASIC SITE CONTAINING REMARK 210 DUPLEX OLIGONUCLEOTIDE; 10 MM REMARK 210 SODIUM PHOSPHATE BUFFER; 3 MM REMARK 210 ABASIC SITE CONTAINING DUPLEX REMARK 210 OLIGONUCLEOTIDE; 10 MM SODIUM REMARK 210 PHOSPHATE BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY, PE-COSY, WATERGATE- REMARK 210 NOESY, 31P-HCOSY, 31P- REMARK 210 DECOUPLED-PE-COSY, 31P- REMARK 210 DECOUPLED-J-SCALED-DQCOSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ, 600 MHZ REMARK 210 SPECTROMETER MODEL : HOME-BUILT REMARK 210 SPECTROMETER MANUFACTURER : HOME-BUILT REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.851, FELIX 95.0 REMARK 210 METHOD USED : MOLECULAR DYNAMICS 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: THE ABASIC SITE DEOXYRIBOSE 1H-1H COUPLING CONSTANTS REMARK 210 AND THE DNA 31P-H3' COUPLING CONSTANTS WERE EXPERIMENTALLY REMARK 210 DETERMINED. THIS INFORMATION WAS USED IN THE MODELING PROTOCOL.
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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 RES CSSEQI ATOMS REMARK 470 AAB A 7 O1P
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 4 N9 DA A 4 C4 0.039 REMARK 500 DT A 10 C5' DT A 10 C4' 0.043 REMARK 500 DT B 22 N1 DT B 22 C2 0.049 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 3 N1 - C6 - N6 ANGL. DEV. = 4.2 DEGREES REMARK 500 DA A 5 N1 - C6 - N6 ANGL. DEV. = 5.5 DEGREES REMARK 500 DA A 5 C5 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 DG A 6 N3 - C2 - N2 ANGL. DEV. = 4.7 DEGREES REMARK 500 DA A 8 N1 - C6 - N6 ANGL. DEV. = 5.7 DEGREES REMARK 500 DG A 12 N3 - C2 - N2 ANGL. DEV. = 4.8 DEGREES REMARK 500 DG A 13 N3 - C2 - N2 ANGL. DEV. = 5.3 DEGREES REMARK 500 DA B 17 N1 - C6 - N6 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG B 18 N3 - C2 - N2 ANGL. DEV. = 5.0 DEGREES REMARK 500 DA B 17 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 DA B 20 N1 - C6 - N6 ANGL. DEV. = 4.3 DEGREES REMARK 500 DC B 21 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC B 21 C3' - O3' - P ANGL. DEV. = 9.3 DEGREES REMARK 500 DT B 22 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 DG B 25 N3 - C2 - N2 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG B 26 N3 - C2 - N2 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 DA A 8 0.08 SIDE_CHAIN REMARK 500 DG A 11 0.09 SIDE_CHAIN REMARK 500 DT B 22 0.07 SIDE_CHAIN REMARK 500 DG B 25 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1A9I RELATED DB: PDB REMARK 900 APYRIMIDINIC DNA WITH BOUND WATER AT THE DAMAGED SITE, REMARK 900 ALPHA FORM, NMR, 1 STRUCTURE REMARK 900 RELATED ID: 1A9J RELATED DB: PDB REMARK 900 APYRIMIDINIC DNA WITH BOUND WATER AT THE DAMAGED SITE, BETA REMARK 900 FORM, NMR, 1 STRUCTURE REMARK 900 RELATED ID: 1G5E RELATED DB: PDB REMARK 900 ENSEMBLE: NMR STRUCTURE OF AN OLIGONUCLEOTIDE CONTAINING AN REMARK 900 ABASIC SITE: BETA ANOMER REMARK 900 RELATED ID: 1G5D RELATED DB: PDB REMARK 900 ENSEMBLE: NMR STRUCTURE OF AN OLIGONUCLEOTIDE CONTAINING AN REMARK 900 ABASIC SITE: ALPHA ANOMER REMARK 900 RELATED ID: 1GIZ RELATED DB: PDB REMARK 900 MINIMIZED AVERAGE STRUCTURE: NMR STRUCTURE OF AN REMARK 900 OLIGONUCLEOTIDE CONTAINING AN ABASIC SITE: ALPHA ANOMER
DBREF 1GJ0 A 1 13 PDB 1GJ0 1GJ0 1 13 DBREF 1GJ0 B 14 26 PDB 1GJ0 1GJ0 14 26
SEQRES 1 A 13 DC DC DA DA DA DG AAB DA DC DT DG DG DG SEQRES 1 B 13 DC DC DC DA DG DT DA DC DT DT DT DG DG
HET AAB A 7 20
HETNAM AAB 2-DEOXY-5-PHOSPHORIBOSE GROUP
FORMUL 1 AAB C5 H11 O7 P
LINK O3' DG A 6 P AAB A 7 1555 1555 1.59 LINK O3' AAB A 7 P DA A 8 1555 1555 1.58
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