Header list of 1n0k.pdb file
Complete list - 23 202 Bytes
HEADER DNA 14-OCT-02 1N0K
TITLE NMR STRUCTURE OF DUPLEX DNA D(CCAAGGXCTTGGG), X IS A 3'
TITLE 2 PHOSPHOGLYCOLATE, 5'PHOSPHATE GAPPED LESION
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*CP*CP*AP*AP*GP*G)-3';
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: 5'-D(P*CP*TP*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*AP*GP*GP*CP*CP*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, BLEOMYCIN, PHOSPHOGLYCOLATE
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR H.-D.JUNKER,S.T.HOEHN,R.C.BUNT,V.MARATHIUS,J.CHEN,C.J.TURNER,J.STUBBE
REVDAT 3 23-FEB-22 1N0K 1 REMARK LINK
REVDAT 2 24-FEB-09 1N0K 1 VERSN
REVDAT 1 07-JAN-03 1N0K 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 OF
JRNL TITL 2 TETHERED OLIGONUCLEOTIDES CONTAINING AN INTERNAL
JRNL TITL 3 3'-PHOSPHOGLYCOLATE, 5'-PHOSPHATE GAPPED 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 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XPLOR 3.851
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1N0K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-OCT-02.
REMARK 100 THE DEPOSITION ID IS D_1000017368.
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 ATM
REMARK 210 SAMPLE CONTENTS : 1.4 MM OLIGONUCLEOTIDE
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : PECOSY; TOCSY; NOESY; HSQC; GE
REMARK 210 -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 : XPLOR 3.851
REMARK 210 METHOD USED : CONJUGATE GRADIENT
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 10
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : MINIMUM RMSD AND NMR CONSTRAINTS
REMARK 210 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 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: TRIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C
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 H41 DC A 1 O6 DG C 26 0.69
REMARK 500 N3 DC A 1 H1 DG C 26 0.76
REMARK 500 O2 DC A 1 H21 DG C 26 1.02
REMARK 500 H41 DC A 1 C6 DG C 26 1.19
REMARK 500 N4 DC A 1 O6 DG C 26 1.38
REMARK 500 C4 DC A 1 H1 DG C 26 1.39
REMARK 500 O4 DT B 10 H61 DA C 17 1.55
REMARK 500 C2 DC A 1 H21 DG C 26 1.59
REMARK 500 O6 DG B 13 H41 DC C 14 1.60
REMARK 500 H42 DC A 1 O6 DG C 26 1.60
REMARK 500 N3 DC A 1 N1 DG C 26 1.66
REMARK 500 O2 DC A 1 N2 DG C 26 1.72
REMARK 500 N4 DC A 1 C6 DG C 26 2.03
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 DC A 1 C2 DC A 1 O2 -0.057
REMARK 500 DC A 1 N1 DC A 1 C6 -0.047
REMARK 500 DC A 1 N3 DC A 1 C4 -0.067
REMARK 500 DA A 4 N9 DA A 4 C4 0.037
REMARK 500 DC B 8 P DC B 8 OP1 0.124
REMARK 500 DC B 8 P DC B 8 OP2 0.125
REMARK 500 DC B 8 P DC B 8 O5' -0.153
REMARK 500 DC B 8 O3' DC B 8 C3' -0.055
REMARK 500 DC B 8 O3' DT B 9 P -0.127
REMARK 500 DT B 9 P DT B 9 OP1 -0.121
REMARK 500 DT B 9 P DT B 9 OP2 -0.108
REMARK 500 DT B 9 C6 DT B 9 N1 0.044
REMARK 500 DT B 10 P DT B 10 O5' -0.086
REMARK 500 DT B 10 O4' DT B 10 C1' -0.073
REMARK 500 DT B 10 O3' DT B 10 C3' -0.044
REMARK 500 DT B 10 C5 DT B 10 C7 -0.038
REMARK 500 DT B 10 O3' DG B 11 P -0.090
REMARK 500 DG B 13 C4' DG B 13 C3' -0.064
REMARK 500 DG B 13 O3' DG B 13 C3' -0.077
REMARK 500 DC C 14 O5' DC C 14 C5' -0.231
REMARK 500 DC C 14 O3' DC C 15 P -0.090
REMARK 500 DC C 15 P DC C 15 O5' -0.070
REMARK 500 DC C 15 O3' DC C 16 P -0.075
REMARK 500 DC C 21 O5' DC C 21 C5' -0.167
REMARK 500 DC C 21 C2' DC C 21 C1' 0.066
REMARK 500 DT C 24 N1 DT C 24 C2 0.055
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 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 DC A 1 C6 - N1 - C2 ANGL. DEV. = -3.4 DEGREES
REMARK 500 DC A 1 C4 - C5 - C6 ANGL. DEV. = 3.4 DEGREES
REMARK 500 DC A 1 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES
REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 DC A 2 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES
REMARK 500 DA A 3 C3' - O3' - P ANGL. DEV. = 10.7 DEGREES
REMARK 500 DC B 8 P - O5' - C5' ANGL. DEV. = 12.7 DEGREES
REMARK 500 DC B 8 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DC B 8 N1 - C2 - O2 ANGL. DEV. = 4.7 DEGREES
REMARK 500 DC B 8 C3' - O3' - P ANGL. DEV. = 9.6 DEGREES
REMARK 500 DT B 9 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES
REMARK 500 DT B 9 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 DT B 10 P - O5' - C5' ANGL. DEV. = 15.5 DEGREES
REMARK 500 DT B 10 C1' - O4' - C4' ANGL. DEV. = 4.4 DEGREES
REMARK 500 DT B 10 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES
REMARK 500 DT B 10 C4 - C5 - C7 ANGL. DEV. = -4.9 DEGREES
REMARK 500 DG B 11 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES
REMARK 500 DG B 11 N3 - C2 - N2 ANGL. DEV. = 5.1 DEGREES
REMARK 500 DG B 12 P - O5' - C5' ANGL. DEV. = 13.0 DEGREES
REMARK 500 DG B 12 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 DG B 12 N3 - C2 - N2 ANGL. DEV. = 5.8 DEGREES
REMARK 500 DG B 13 C1' - O4' - C4' ANGL. DEV. = 6.2 DEGREES
REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES
REMARK 500 DG B 13 C2 - N3 - C4 ANGL. DEV. = 3.4 DEGREES
REMARK 500 DG B 13 N3 - C4 - C5 ANGL. DEV. = -3.3 DEGREES
REMARK 500 DG B 13 N1 - C2 - N2 ANGL. DEV. = -6.2 DEGREES
REMARK 500 DG B 13 N3 - C2 - N2 ANGL. DEV. = 8.5 DEGREES
REMARK 500 DC C 14 N1 - C2 - O2 ANGL. DEV. = 4.6 DEGREES
REMARK 500 DC C 15 C6 - N1 - C2 ANGL. DEV. = -3.5 DEGREES
REMARK 500 DC C 15 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES
REMARK 500 DC C 16 C6 - N1 - C2 ANGL. DEV. = -2.7 DEGREES
REMARK 500 DC C 16 C3' - O3' - P ANGL. DEV. = 10.0 DEGREES
REMARK 500 DA C 17 C3' - O3' - P ANGL. DEV. = 9.4 DEGREES
REMARK 500 DA C 18 N1 - C6 - N6 ANGL. DEV. = 4.1 DEGREES
REMARK 500 DA C 18 C3' - O3' - P ANGL. DEV. = 9.0 DEGREES
REMARK 500 DG C 19 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES
REMARK 500 DG C 19 N3 - C2 - N2 ANGL. DEV. = 5.3 DEGREES
REMARK 500 DG C 19 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES
REMARK 500 DG C 20 C1' - O4' - C4' ANGL. DEV. = 5.4 DEGREES
REMARK 500 DG C 20 C3' - C2' - C1' ANGL. DEV. = 9.3 DEGREES
REMARK 500 DG C 20 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 DG C 20 N3 - C2 - N2 ANGL. DEV. = 4.9 DEGREES
REMARK 500 DC C 21 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES
REMARK 500 DC C 22 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES
REMARK 500 DT C 23 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 DT C 24 C3' - O3' - P ANGL. DEV. = 8.6 DEGREES
REMARK 500 DG C 26 C2 - N3 - C4 ANGL. DEV. = 3.0 DEGREES
REMARK 500 DG C 26 N3 - C2 - N2 ANGL. DEV. = 4.7 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 DA A 3 0.16 SIDE CHAIN
REMARK 500 DG A 6 0.05 SIDE CHAIN
REMARK 500 DT B 9 0.08 SIDE CHAIN
REMARK 500 DT B 10 0.07 SIDE CHAIN
REMARK 500 DG B 11 0.07 SIDE CHAIN
REMARK 500 DC C 15 0.12 SIDE CHAIN
REMARK 500 DC C 16 0.19 SIDE CHAIN
REMARK 500 DA C 17 0.06 SIDE CHAIN
REMARK 500 DG C 19 0.06 SIDE CHAIN
REMARK 500 DT C 23 0.15 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 PGA A 7
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1N0O RELATED DB: PDB
REMARK 900 THIS ENTRY IS THE ENSEMBLE MODEL FOR PDB ENTRY 1N0K
REMARK 900 RELATED ID: 1G5K RELATED DB: PDB
REMARK 900 ENSEMBLE: 1G5K IS THE STRUCTURE OF THE OLIGONUCLEOTIDE CONTAINING
REMARK 900 THE PHOSPHOGLYCOLATE LESION WITHOUT THE BLEOMYCIN BOUND.
REMARK 900 RELATED ID: 1GJ1 RELATED DB: PDB
REMARK 900 MINIMIZED AVERAGE STRUCTURE: NMR STRUCTURE OF AN OLIGONUCLEOTIDE
REMARK 900 CONTAINING A PHOSPHOGLYCOLATE LESION
DBREF 1N0K A 1 6 PDB 1N0K 1N0K 1 6
DBREF 1N0K B 8 13 PDB 1N0K 1N0K 8 13
DBREF 1N0K C 14 26 PDB 1N0K 1N0K 14 26
SEQRES 1 A 6 DC DC DA DA DG DG
SEQRES 1 B 6 DC DT DT DG DG DG
SEQRES 1 C 13 DC DC DC DA DA DG DG DC DC 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 1.62
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
Complete list - 23 202 Bytes