Header list of 1a9h.pdb file
Complete list - 22 201 Bytes
HEADER DNA 06-APR-98 1A9H TITLE APURINIC DNA WITH BOUND WATER AT THE DAMAGED SITE AND O2 OF CYTOSINE, TITLE 2 BETA FORM, 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*CP*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, APURINIC DNA, WATER, DNA EXPDTA SOLUTION NMR AUTHOR R.D.BEGER,P.H.BOLTON REVDAT 3 09-JUL-14 1A9H 1 HETNAM VERSN REVDAT 2 24-FEB-09 1A9H 1 VERSN REVDAT 1 15-JUL-98 1A9H 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 1A9H 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: 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 O1' AAB A 6 H1 HOH A 23 1.59 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 C5' DC A 1 C4' -0.085 REMARK 500 DC A 1 C4' DC A 1 C3' -0.090 REMARK 500 DC A 1 C3' DC A 1 C2' -0.131 REMARK 500 DC A 1 C2' DC A 1 C1' -0.121 REMARK 500 DC A 1 O4' DC A 1 C4' -0.158 REMARK 500 DC A 1 C1' DC A 1 N1 -0.085 REMARK 500 DC A 1 C4 DC A 1 N4 -0.091 REMARK 500 DC A 1 N1 DC A 1 C6 -0.037 REMARK 500 DC A 1 C2 DC A 1 N3 -0.085 REMARK 500 DC A 1 C5 DC A 1 C6 -0.082 REMARK 500 DG A 2 P DG A 2 OP1 -0.162 REMARK 500 DG A 2 P DG A 2 OP2 -0.177 REMARK 500 DG A 2 P DG A 2 O5' -0.108 REMARK 500 DG A 2 C5' DG A 2 C4' -0.089 REMARK 500 DG A 2 C3' DG A 2 C2' -0.061 REMARK 500 DG A 2 C2' DG A 2 C1' -0.063 REMARK 500 DG A 2 O4' DG A 2 C4' -0.065 REMARK 500 DG A 2 C2 DG A 2 N3 -0.054 REMARK 500 DG A 2 C5 DG A 2 N7 -0.038 REMARK 500 DG A 2 N9 DG A 2 C4 -0.070 REMARK 500 DC A 3 P DC A 3 OP2 -0.151 REMARK 500 DC A 3 P DC A 3 O5' -0.104 REMARK 500 DC A 3 C5' DC A 3 C4' -0.085 REMARK 500 DC A 3 O3' DC A 3 C3' -0.037 REMARK 500 DC A 3 C2 DC A 3 O2 -0.062 REMARK 500 DC A 3 N1 DC A 3 C2 -0.065 REMARK 500 DC A 3 N1 DC A 3 C6 -0.057 REMARK 500 DC A 3 N3 DC A 3 C4 -0.055 REMARK 500 DC A 3 C4 DC A 3 C5 -0.051 REMARK 500 DG A 9 P DG A 9 OP1 -0.103 REMARK 500 DG A 9 P DG A 9 OP2 -0.119 REMARK 500 DG A 9 C3' DG A 9 C2' -0.090 REMARK 500 DG A 9 C2' DG A 9 C1' -0.091 REMARK 500 DG A 9 O4' DG A 9 C1' -0.077 REMARK 500 DG A 9 O4' DG A 9 C4' -0.077 REMARK 500 DG A 9 N1 DG A 9 C2 -0.058 REMARK 500 DG A 9 C4 DG A 9 C5 -0.069 REMARK 500 DG A 9 N7 DG A 9 C8 -0.048 REMARK 500 DG A 9 C8 DG A 9 N9 -0.043 REMARK 500 DG A 9 C6 DG A 9 O6 -0.061 REMARK 500 DC A 8 O3' DG A 9 P -0.079 REMARK 500 DC A 10 P DC A 10 O5' -0.073 REMARK 500 DC A 10 O5' DC A 10 C5' -0.238 REMARK 500 DC A 10 C3' DC A 10 C2' -0.073 REMARK 500 DC A 10 C2' DC A 10 C1' -0.084 REMARK 500 DC A 10 O4' DC A 10 C4' -0.081 REMARK 500 DC A 10 N1 DC A 10 C2 -0.068 REMARK 500 DC A 10 C4 DC A 10 C5 -0.058 REMARK 500 DC A 11 C3' DC A 11 C2' -0.053 REMARK 500 DC A 11 C2 DC A 11 O2 -0.060 REMARK 500 REMARK 500 THIS ENTRY HAS 94 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' - C4' - C3' ANGL. DEV. = 4.3 DEGREES REMARK 500 DC A 1 O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES REMARK 500 DC A 1 C6 - N1 - C2 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC A 1 N1 - C2 - O2 ANGL. DEV. = 5.5 DEGREES REMARK 500 DG A 2 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 DG A 2 C4' - C3' - C2' ANGL. DEV. = -6.0 DEGREES REMARK 500 DC A 3 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES REMARK 500 DC A 3 N3 - C4 - C5 ANGL. DEV. = -2.6 DEGREES REMARK 500 DG A 2 C3' - O3' - P ANGL. DEV. = 7.9 DEGREES REMARK 500 DG A 4 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC A 3 C3' - O3' - P ANGL. DEV. = 10.4 DEGREES REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC A 8 O4' - C1' - C2' ANGL. DEV. = -8.6 DEGREES REMARK 500 DG A 9 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC A 10 P - O5' - C5' ANGL. DEV. = 16.3 DEGREES REMARK 500 DC A 10 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC A 11 C4' - C3' - C2' ANGL. DEV. = -4.4 DEGREES REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG B 12 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC B 19 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG B 20 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC B 19 C3' - O3' - P ANGL. DEV. = 12.2 DEGREES REMARK 500 DC B 21 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG B 22 O4' - C4' - C3' ANGL. DEV. = -5.1 DEGREES REMARK 500 DG B 22 C5' - C4' - O4' ANGL. DEV. = 6.7 DEGREES REMARK 500 DG B 22 O4' - C1' - N9 ANGL. DEV. = 8.5 DEGREES REMARK 500 DC B 21 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 1A9H A 1 11 PDB 1A9H 1A9H 1 11 DBREF 1A9H B 12 22 PDB 1A9H 1A9H 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 DC 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 1.59 LINK O3' AAB A 6 P DA A 7 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
Complete list - 22 201 Bytes