Header list of 1a9i.pdb file
Complete list - 22 201 Bytes
HEADER DNA 06-APR-98 1A9I
TITLE APYRIMIDINIC DNA WITH BOUND WATER AT THE DAMAGED SITE, ALPHA FORM,
TITLE 2 NMR, 1 STRUCTURE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*GP*AP*AABP*AP*CP*GP*CP*C)-3');
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: DNA (5'-D(*GP*GP*CP*GP*TP*AP*TP*CP*GP*CP*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 DAMAGED DNA, APYRIMIDINIC DNA, WATER, DNA
EXPDTA SOLUTION NMR
AUTHOR R.D.BEGER,P.H.BOLTON
REVDAT 3 09-JUL-14 1A9I 1 HETNAM VERSN
REVDAT 2 24-FEB-09 1A9I 1 VERSN
REVDAT 1 15-JUL-98 1A9I 0
JRNL AUTH R.D.BEGER,P.H.BOLTON
JRNL TITL STRUCTURES OF APURINIC AND APYRIMIDINIC SITES IN DUPLEX
JRNL TITL 2 DNAS.
JRNL REF J.BIOL.CHEM. V. 273 15565 1998
JRNL REFN ISSN 0021-9258
JRNL PMID 9624147
JRNL DOI 10.1074/JBC.273.25.15565
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.1
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1A9I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 300
REMARK 210 PH : 7.0
REMARK 210 IONIC STRENGTH : 50 MM KCL
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : TRIS
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; PECOSY; TOCSY; ROESY;
REMARK 210 QUIET-NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 400 MHZ; 500 MHZ
REMARK 210 SPECTROMETER MODEL : UNITY+; INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : VNMR
REMARK 210 METHOD USED : MATRIX RELAXATION
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : AVERAGE OF 5 STRUCTURES THAT THE
REMARK 210 NOESY BACKCALCULATION AGREES WITH
REMARK 210 EXPERIMENTAL NOESY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: 100MS NOESY, 250MS NOESY 250MS QUIETNOESY 70MS BAND-
REMARK 210 SELECTIVE J TOCSY FOR PHOSPHOROUS "J SCALE" SET TO 2 AND 3
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 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 6 O3P
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 C4' DC A 1 C3' -0.153
REMARK 500 DC A 1 C3' DC A 1 C2' -0.101
REMARK 500 DC A 1 C2' DC A 1 C1' -0.094
REMARK 500 DC A 1 O4' DC A 1 C1' -0.110
REMARK 500 DC A 1 O4' DC A 1 C4' -0.067
REMARK 500 DC A 1 O3' DC A 1 C3' -0.082
REMARK 500 DC A 1 C2 DC A 1 O2 -0.103
REMARK 500 DC A 1 C4 DC A 1 N4 -0.085
REMARK 500 DC A 1 N1 DC A 1 C6 -0.099
REMARK 500 DC A 1 C2 DC A 1 N3 -0.079
REMARK 500 DC A 1 N3 DC A 1 C4 -0.101
REMARK 500 DC A 1 C5 DC A 1 C6 -0.073
REMARK 500 DG A 2 P DG A 2 OP1 -0.194
REMARK 500 DG A 2 P DG A 2 OP2 -0.178
REMARK 500 DG A 2 P DG A 2 O5' -0.139
REMARK 500 DG A 2 C4' DG A 2 C3' -0.061
REMARK 500 DG A 2 C2' DG A 2 C1' -0.071
REMARK 500 DG A 2 O3' DG A 2 C3' -0.038
REMARK 500 DG A 2 N9 DG A 2 C4 -0.050
REMARK 500 DC A 1 O3' DG A 2 P -0.261
REMARK 500 DG A 4 O3' DG A 4 C3' -0.037
REMARK 500 DA A 5 P DA A 5 OP1 -0.112
REMARK 500 DA A 5 P DA A 5 OP2 -0.110
REMARK 500 DA A 7 P DA A 7 OP1 -0.104
REMARK 500 DC A 8 P DC A 8 OP1 -0.107
REMARK 500 DC A 8 P DC A 8 O5' -0.119
REMARK 500 DA A 7 O3' DC A 8 P -0.127
REMARK 500 DC A 11 P DC A 11 OP1 -0.284
REMARK 500 DC A 11 P DC A 11 OP2 -0.349
REMARK 500 DC A 11 P DC A 11 O5' -0.359
REMARK 500 DC A 11 C2' DC A 11 C1' -0.073
REMARK 500 DC A 11 O3' DC A 11 C3' -0.045
REMARK 500 DC A 11 C2 DC A 11 O2 -0.065
REMARK 500 DC A 11 N1 DC A 11 C2 -0.073
REMARK 500 DC A 11 N1 DC A 11 C6 -0.058
REMARK 500 DC A 11 N3 DC A 11 C4 -0.056
REMARK 500 DC A 11 C4 DC A 11 C5 -0.053
REMARK 500 DG B 12 C5' DG B 12 C4' -0.184
REMARK 500 DG B 12 C4' DG B 12 C3' -0.077
REMARK 500 DG B 12 O4' DG B 12 C4' -0.069
REMARK 500 DT B 16 P DT B 16 OP1 -0.146
REMARK 500 DT B 16 P DT B 16 O5' -0.077
REMARK 500 DT B 16 C5 DT B 16 C7 0.038
REMARK 500 DG B 15 O3' DT B 16 P -0.124
REMARK 500 DT B 18 O3' DC B 19 P -0.084
REMARK 500 DC B 21 C3' DC B 21 C2' -0.071
REMARK 500 DG B 22 P DG B 22 OP1 -0.126
REMARK 500 DG B 22 P DG B 22 OP2 -0.180
REMARK 500 DG B 22 P DG B 22 O5' -0.203
REMARK 500 DG B 22 C5' DG B 22 C4' -0.121
REMARK 500
REMARK 500 THIS ENTRY HAS 63 BOND DEVIATIONS.
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' - C2' ANGL. DEV. = -8.2 DEGREES
REMARK 500 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 DC A 1 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES
REMARK 500 DC A 1 N3 - C2 - O2 ANGL. DEV. = -5.7 DEGREES
REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES
REMARK 500 DC A 1 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES
REMARK 500 DC A 3 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES
REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 DA A 7 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES
REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES
REMARK 500 DC A 8 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES
REMARK 500 DC A 11 P - O5' - C5' ANGL. DEV. = 22.5 DEGREES
REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES
REMARK 500 DC A 11 N3 - C4 - C5 ANGL. DEV. = -2.7 DEGREES
REMARK 500 DG B 12 O4' - C4' - C3' ANGL. DEV. = 7.0 DEGREES
REMARK 500 DG B 12 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DT B 16 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES
REMARK 500 DG B 15 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES
REMARK 500 DA B 17 C4' - C3' - C2' ANGL. DEV. = -4.4 DEGREES
REMARK 500 DT B 18 O4' - C1' - C2' ANGL. DEV. = -6.9 DEGREES
REMARK 500 DT B 18 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 DA B 17 C3' - O3' - P ANGL. DEV. = 9.7 DEGREES
REMARK 500 DC B 19 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DG B 20 C3' - O3' - P ANGL. DEV. = 9.2 DEGREES
REMARK 500 DG B 22 C4' - C3' - C2' ANGL. DEV. = -4.6 DEGREES
REMARK 500 DG B 22 O4' - C1' - C2' ANGL. DEV. = -6.1 DEGREES
REMARK 500 DG B 22 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DG B 22 C4 - C5 - N7 ANGL. DEV. = -2.5 DEGREES
REMARK 500 DG B 22 N1 - C6 - O6 ANGL. DEV. = -4.0 DEGREES
REMARK 500 DC B 21 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1A9I A 1 11 PDB 1A9I 1A9I 1 11
DBREF 1A9I B 12 22 PDB 1A9I 1A9I 12 22
SEQRES 1 A 11 DC DG DC DG DA AAB DA DC DG DC DC
SEQRES 1 B 11 DG DG DC DG DT DA DT DC DG DC DG
HET AAB A 6 20
HETNAM AAB 2'-DEOXY-RIBOFURANOSE-5'-MONOPHOSPHATE
HETSYN AAB ABASIC DEOXYRIBOSE
FORMUL 1 AAB C5 H11 O7 P
FORMUL 3 HOH *(H2 O)
LINK P AAB A 6 O3' DA A 5 1555 1555 1.54
LINK O3' AAB A 6 P DA A 7 1555 1555 1.57
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 - 22 201 Bytes