10 20 30 40 50 60 70 80 1GJ1 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 14-OCT-02 1GJ1
TITLE NMR STRUCTURE OF D(CCAAAGXACTGGG), X IS A TITLE 2 3'PHOSPHOGLYCOLATE, 5'PHOSPHATE GAPPED LESION
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*AP*AP*AP*G)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(P*AP*CP*TP*GP*GP*G)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: 5'-D(*CP*CP*CP*AP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3'; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 SYNTHETIC: YES
KEYWDS DNA, NMR, BLEOMYCIN, PHOSPHOGLYCOLATE
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR H.-D.JUNKER,S.T.HOEHN,R.C.BUNT,V.MARATHIUS,J.CHEN, AUTHOR 2 C.J.TURNER,J.STUBBE
REVDAT 2 24-FEB-09 1GJ1 1 VERSN REVDAT 1 07-JAN-03 1GJ1 0
JRNL AUTH H.-D.JUNKER,S.T.HOEHN,R.C.BUNT,V.MARATHIUS,J.CHEN, JRNL AUTH 2 C.J.TURNER,J.STUBBE JRNL TITL SYNTHESIS, CHARACTERIZATION AND SOLUTION STRUCTURE JRNL TITL 2 OF TETHERED OLIGONUCLEOTIDES CONTAINING AN JRNL TITL 3 INTERNAL 3'-PHOSPHOGLYCOLATE, 5'-PHOSPHATE GAPPED JRNL TITL 4 LESION JRNL REF NUCLEIC ACIDS RES. V. 30 5497 2002 JRNL REFN ISSN 0305-1048 JRNL PMID 12490718 JRNL DOI 10.1093/NAR/GKF681
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: NULL
REMARK 4 REMARK 4 1GJ1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-NOV-02. REMARK 100 THE RCSB ID CODE IS RCSB017370.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293.15 REMARK 210 PH : 6.9 REMARK 210 IONIC STRENGTH : 40 MM NAH2PO4 REMARK 210 PRESSURE : 1.0 ATM REMARK 210 SAMPLE CONTENTS : 1.4 MM OLIGONUCLEOTIDE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : PECOSY, TOCSY, NOESY, HSQC, REMARK 210 GE-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 600 MHZ, 750 MHZ REMARK 210 SPECTROMETER MODEL : CUSTOM BUILD REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.851 REMARK 210 METHOD USED : CONJUGATE GRADIENT REMARK 210 MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : MINIMUM RMSD AND NMR REMARK 210 CONSTRAINTS VIOLATION 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 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 B 8 P DA B 8 OP3 -0.128 REMARK 500 DT B 10 N1 DT B 10 C2 0.054 REMARK 500 DG B 11 C5' DG B 11 C4' 0.042 REMARK 500 DT C 19 N1 DT C 19 C2 0.053 REMARK 500 DT C 23 C5' DT C 23 C4' 0.046 REMARK 500 DT C 24 C5' DT C 24 C4' 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 DC A 1 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC A 1 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 DA A 3 N1 - C6 - N6 ANGL. DEV. = 5.0 DEGREES REMARK 500 DC A 2 C3' - O3' - P ANGL. DEV. = 7.9 DEGREES REMARK 500 DA A 3 C3' - O3' - P ANGL. DEV. = 9.7 DEGREES REMARK 500 DA A 5 N1 - C6 - N6 ANGL. DEV. = 4.7 DEGREES REMARK 500 DA B 8 N1 - C6 - N6 ANGL. DEV. = 4.3 DEGREES REMARK 500 DC B 9 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG B 11 N3 - C2 - N2 ANGL. DEV. = 6.5 DEGREES REMARK 500 DT B 10 C3' - O3' - P ANGL. DEV. = 10.9 DEGREES REMARK 500 DG B 12 N3 - C2 - N2 ANGL. DEV. = 5.0 DEGREES REMARK 500 DG B 13 N3 - C2 - N2 ANGL. DEV. = 5.3 DEGREES REMARK 500 DC C 14 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC C 16 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC C 16 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES REMARK 500 DG C 18 N3 - C2 - N2 ANGL. DEV. = 4.9 DEGREES REMARK 500 DA C 17 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 DT C 19 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 DT C 19 C3' - O3' - P ANGL. DEV. = 9.1 DEGREES REMARK 500 DT C 22 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT C 23 C4 - C5 - C7 ANGL. DEV. = 3.6 DEGREES REMARK 500 DT C 23 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 DG C 25 N3 - C2 - N2 ANGL. DEV. = 5.1 DEGREES REMARK 500 DG C 26 N3 - C2 - N2 ANGL. DEV. = 5.4 DEGREES REMARK 500 DG C 25 C3' - O3' - P ANGL. DEV. = 9.7 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 0.06 SIDE_CHAIN REMARK 500 DA A 3 0.06 SIDE_CHAIN REMARK 500 DA A 4 0.08 SIDE_CHAIN REMARK 500 DC B 9 0.08 SIDE_CHAIN REMARK 500 DG B 11 0.07 SIDE_CHAIN REMARK 500 DG B 12 0.13 SIDE_CHAIN REMARK 500 DC C 15 0.09 SIDE_CHAIN REMARK 500 DC C 16 0.06 SIDE_CHAIN REMARK 500 DG C 18 0.10 SIDE_CHAIN REMARK 500 DT C 19 0.08 SIDE_CHAIN REMARK 500 DT C 22 0.07 SIDE_CHAIN REMARK 500 DT C 23 0.10 SIDE_CHAIN REMARK 500 DT C 24 0.07 SIDE_CHAIN REMARK 500 DG C 25 0.06 SIDE_CHAIN REMARK 500 DG C 26 0.08 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PGA A 7
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGA A 7
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1N0O RELATED DB: PDB REMARK 900 ENSEMBLE MODEL OF PDB ENTRY 1N0K REMARK 900 RELATED ID: 1N0K RELATED DB: PDB REMARK 900 MINIMIZED AVERAGE STRUCTURE OF PDB ENTRY 1N0O REMARK 900 RELATED ID: 1G5K RELATED DB: PDB REMARK 900 ENSEMBLE: 1G5K IS THE STRUCTURE OF THE OLIGONUCLEOTIDE REMARK 900 CONTAINING THE PHOSPHOGLYCOLATE LESION WITHOUT THE REMARK 900 BLEOMYCIN BOUND.
DBREF 1GJ1 A 1 6 PDB 1GJ1 1GJ1 1 6 DBREF 1GJ1 B 8 13 PDB 1GJ1 1GJ1 8 13 DBREF 1GJ1 C 14 26 PDB 1GJ1 1GJ1 14 26
SEQRES 1 A 6 DC DC DA DA DA DG SEQRES 1 B 6 DA DC DT DG DG DG SEQRES 1 C 13 DC DC DC DA DG DT DA DC DT DT DT DG DG
HET PGA A 7 10
HETNAM PGA 2-PHOSPHOGLYCOLIC ACID
FORMUL 4 PGA C2 H5 O6 P
LINK O3' DG A 6 P PGA A 7 1555 1555 1.58
SITE 1 AC1 1 DG A 6
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