Header list of 1sjk.pdb file
Complete list - 2 202 Bytes
HEADER DNA 22-JUL-97 1SJK
TITLE A DUPLEX DNA WITH AN ABASIC SITE IN A DA TRACT, ALPHA FORM, NMR,
TITLE 2 MINIMIZED AVERAGE STRUCTURE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*AP*AP*AP*AP*AP*TP*GP*CP*G)-3');
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: DNA (5'-D(*CP*GP*CP*AP*TP*TP*ORPP*TP*TP*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 DUPLEX DNA WITH AN ABASIC SITE IN A DA TRACT, DAMAGED DNA, AT TRACT
KEYWDS 2 DNA, DEOXYRIBONUCLEIC ACID, DNA
EXPDTA SOLUTION NMR
AUTHOR K.Y.WANG,S.A.PARKER,I.GOLJER,P.H.BOLTON
REVDAT 3 02-MAR-22 1SJK 1 REMARK LINK
REVDAT 2 24-FEB-09 1SJK 1 VERSN
REVDAT 1 03-DEC-97 1SJK 0
JRNL AUTH K.Y.WANG,S.A.PARKER,I.GOLJER,P.H.BOLTON
JRNL TITL SOLUTION STRUCTURE OF A DUPLEX DNA WITH AN ABASIC SITE IN A
JRNL TITL 2 DA TRACT.
JRNL REF BIOCHEMISTRY V. 36 11629 1997
JRNL REFN ISSN 0006-2960
JRNL PMID 9305952
JRNL DOI 10.1021/BI971464L
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 1SJK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000176390.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : NULL
REMARK 210 PH : NULL
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL
REMARK 210 SPECTROMETER FIELD STRENGTH : NULL
REMARK 210 SPECTROMETER MODEL : NULL
REMARK 210 SPECTROMETER MANUFACTURER : NULL
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : NULL
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 6
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: THIS IS THE AVERAGE OF SIX STRUCTURES CALCULATED AT 2PS
REMARK 210 INTERVALS FROM 70 PICOSECONDS TO 80 PICOSECONDS DURING
REMARK 210 RESTRAINED MOLECULAR DYNAMICS.
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 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 H61 DA A 5 O4 DT B 20 1.48
REMARK 500 H61 DA A 7 O4 DT B 18 1.49
REMARK 500 H61 DA A 4 O4 DT B 21 1.51
REMARK 500 O4 DT A 9 H61 DA B 16 1.52
REMARK 500 H61 DA A 8 O4 DT B 17 1.54
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 O5' DC A 1 C5' -0.361
REMARK 500 DG A 2 P DG A 2 OP2 -0.115
REMARK 500 DA A 5 P DA A 5 OP1 -0.185
REMARK 500 DA A 5 P DA A 5 OP2 -0.178
REMARK 500 DA A 5 P DA A 5 O5' -0.083
REMARK 500 DA A 6 O3' DA A 6 C3' -0.049
REMARK 500 DA A 6 O3' DA A 7 P -0.166
REMARK 500 DA A 7 P DA A 7 OP2 -0.141
REMARK 500 DA A 7 O5' DA A 7 C5' -0.325
REMARK 500 DA A 7 C4' DA A 7 C3' -0.069
REMARK 500 DA A 7 O3' DA A 7 C3' -0.036
REMARK 500 DA A 8 P DA A 8 OP1 -0.334
REMARK 500 DA A 8 P DA A 8 OP2 -0.388
REMARK 500 DA A 8 P DA A 8 O5' -0.332
REMARK 500 DA A 8 O5' DA A 8 C5' -0.300
REMARK 500 DA A 8 C5' DA A 8 C4' -0.099
REMARK 500 DA A 8 C4' DA A 8 C3' -0.076
REMARK 500 DT A 9 P DT A 9 O5' -0.062
REMARK 500 DT A 9 N3 DT A 9 C4 -0.056
REMARK 500 DT B 17 C5 DT B 17 C7 0.055
REMARK 500 DT B 20 C5 DT B 20 C7 0.046
REMARK 500 DT B 21 P DT B 21 O5' -0.099
REMARK 500 DT B 21 C5 DT B 21 C7 0.047
REMARK 500 DG B 22 P DG B 22 OP1 -0.118
REMARK 500 DG B 22 P DG B 22 OP2 -0.132
REMARK 500 DG B 22 P DG B 22 O5' -0.101
REMARK 500 DG B 24 C3' DG B 24 C2' -0.067
REMARK 500 DG B 24 C6 DG B 24 N1 -0.046
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 DG A 2 P - O5' - C5' ANGL. DEV. = 12.9 DEGREES
REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 DG A 2 C3' - O3' - P ANGL. DEV. = 10.9 DEGREES
REMARK 500 DA A 4 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES
REMARK 500 DA A 4 C3' - O3' - P ANGL. DEV. = 9.5 DEGREES
REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES
REMARK 500 DA A 5 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 DA A 5 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES
REMARK 500 DA A 6 P - O5' - C5' ANGL. DEV. = 12.4 DEGREES
REMARK 500 DA A 6 O4' - C4' - C3' ANGL. DEV. = 4.1 DEGREES
REMARK 500 DA A 6 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DA A 6 C3' - O3' - P ANGL. DEV. = 29.1 DEGREES
REMARK 500 DA A 7 O5' - C5' - C4' ANGL. DEV. = 35.3 DEGREES
REMARK 500 DA A 7 P - O5' - C5' ANGL. DEV. = 18.2 DEGREES
REMARK 500 DA A 7 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES
REMARK 500 DA A 8 O5' - P - OP1 ANGL. DEV. = -6.2 DEGREES
REMARK 500 DA A 8 O5' - C5' - C4' ANGL. DEV. = 28.6 DEGREES
REMARK 500 DA A 8 P - O5' - C5' ANGL. DEV. = 15.0 DEGREES
REMARK 500 DA A 8 O4' - C4' - C3' ANGL. DEV. = 8.2 DEGREES
REMARK 500 DA A 8 C4' - C3' - C2' ANGL. DEV. = -4.2 DEGREES
REMARK 500 DA A 8 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES
REMARK 500 DA A 8 C3' - O3' - P ANGL. DEV. = 12.6 DEGREES
REMARK 500 DT A 9 P - O5' - C5' ANGL. DEV. = 10.1 DEGREES
REMARK 500 DT A 9 C5 - C6 - N1 ANGL. DEV. = -3.6 DEGREES
REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DG A 10 C3' - O3' - P ANGL. DEV. = 10.6 DEGREES
REMARK 500 DC A 11 O4' - C4' - C3' ANGL. DEV. = 3.9 DEGREES
REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 DC A 11 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES
REMARK 500 DC A 11 C3' - O3' - P ANGL. DEV. = 12.2 DEGREES
REMARK 500 DG A 12 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES
REMARK 500 DC B 13 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES
REMARK 500 DC B 13 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DC B 13 C2 - N3 - C4 ANGL. DEV. = 4.5 DEGREES
REMARK 500 DC B 13 N1 - C2 - O2 ANGL. DEV. = 5.1 DEGREES
REMARK 500 DG B 14 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES
REMARK 500 DG B 14 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES
REMARK 500 DG B 14 C3' - O3' - P ANGL. DEV. = 9.3 DEGREES
REMARK 500 DA B 16 P - O5' - C5' ANGL. DEV. = 10.4 DEGREES
REMARK 500 DA B 16 O4' - C1' - N9 ANGL. DEV. = 6.8 DEGREES
REMARK 500 DA B 16 N9 - C4 - C5 ANGL. DEV. = 2.6 DEGREES
REMARK 500 DA B 16 C3' - O3' - P ANGL. DEV. = 9.1 DEGREES
REMARK 500 DT B 17 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES
REMARK 500 DT B 18 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 DT B 18 C6 - C5 - C7 ANGL. DEV. = -5.0 DEGREES
REMARK 500 DT B 18 C3' - O3' - P ANGL. DEV. = 8.3 DEGREES
REMARK 500 DT B 20 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES
REMARK 500 DT B 20 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES
REMARK 500 DT B 21 P - O5' - C5' ANGL. DEV. = 14.7 DEGREES
REMARK 500 DT B 21 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 57 ANGLE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1SJL RELATED DB: PDB
REMARK 900 MINIMIZED AVERAGE STRUCTURE
DBREF 1SJK A 1 12 PDB 1SJK 1SJK 1 12
DBREF 1SJK B 13 24 PDB 1SJK 1SJK 13 24
SEQRES 1 A 12 DC DG DC DA DA DA DA DA DT DG DC DG
SEQRES 1 B 12 DC DG DC DA DT DT ORP DT DT DG DC DG
HET ORP B 19 20
HETNAM ORP 2-DEOXY-5-PHOSPHONO-RIBOSE
FORMUL 2 ORP C5 H11 O7 P
LINK O3' DT B 18 P ORP B 19 1555 1555 1.63
LINK O3 ORP B 19 P DT B 20 1555 1555 1.59
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 - 2 202 Bytes