Header list of 108d.pdb file
Complete list - b 16 2 Bytes
HEADER DNA 31-JAN-95 108D
TITLE THE SOLUTION STRUCTURE OF A DNA COMPLEX WITH THE FLUORESCENT BIS
TITLE 2 INTERCALATOR TOTO DETERMINED BY NMR SPECTROSCOPY
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*TP*AP*GP*CP*G)-3');
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED
KEYWDS DNA, FLUORESCENT BIS INTERCALATOR, TOTO, BIS-THIAZOLE ORANGE
EXPDTA SOLUTION NMR
NUMMDL 40
AUTHOR H.P.SPIELMANN,D.E.WEMMER,J.P.JACOBSEN
REVDAT 3 16-FEB-22 108D 1 REMARK
REVDAT 2 24-FEB-09 108D 1 VERSN
REVDAT 1 03-JUN-95 108D 0
JRNL AUTH H.P.SPIELMANN,D.E.WEMMER,J.P.JACOBSEN
JRNL TITL SOLUTION STRUCTURE OF A DNA COMPLEX WITH THE FLUORESCENT
JRNL TITL 2 BIS-INTERCALATOR TOTO DETERMINED BY NMR SPECTROSCOPY.
JRNL REF BIOCHEMISTRY V. 34 8542 1995
JRNL REFN ISSN 0006-2960
JRNL PMID 7612596
JRNL DOI 10.1021/BI00027A004
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : AMBER
REMARK 3 AUTHORS : MOLECULAR SIMULATIONS INC. (DISCOVER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 REFINEMENT WAS BASED ON TOTAL RELAXATION MATRIX ANALYSIS OF THE
REMARK 3 NOESY CROSS PEAK INTENSITIES USING THE PROGRAM MARDIGRAS. IMPROVED
REMARK 3 PROCEDURES TO CONSIDER THE EXPERIMENTAL "NOISE" IN NOESY SPECTRA
REMARK 3 DURING THESE CALCULATIONS HAVE BEEN EMPLOYED (LIU, H., SPIELMANN,
REMARK 3 H.P., WEMMER, D.E., & JAMES, T.L. (1995) IN PREPARATION). THE NOE
REMARK 3 DERIVED DISTANCE RESTRAINTS WERE APPLIED IN RESTRAINED MOLECULAR
REMARK 3 DYNAMICS CALCULATIONS USING THE PROGRAM DISCOVER VERSION 2.9.5
REMARK 3 WITH MODIFIED AMBER FORCE-FIELD POTENTIALS AS IMPLEMENTED IN
REMARK 3 DISCOVER. THE ROOT-MEAN-SQUARE (RMS) DEVIATION OF THE COORDINATES
REMARK 3 FOR THE FORTY STRUCTURES OF THE COMPLEX WAS 1.4 ANGSTROMS
REMARK 3 (INCLUDING THE DISORDERED TERMINAL DNA RESIDUES). THE COMPLEX
REMARK 3 EXHIBITS TWO-FOLD SPECTROSCOPIC SYMMETRY, BUT NO SYMMETRY WAS
REMARK 3 IMPOSED DURING THE REFINEMENT. DEVIATIONS FROM IDEAL TWO-FOLD
REMARK 3 SYMMETRY REFLECT THE UNCERTAINTY IN THE NMR DATA. THE 40
REMARK 3 STRUCTURES ARE BASED ON 362 INTERPROTON DISTANCE RESTRAINTS FROM
REMARK 3 NOE MEASUREMENTS, 22 HYDROGEN BOND DISTANCE RESTRAINTS, AND 48
REMARK 3 RESTRAINTS TO ENFORCE CHIRALITY IN THE DEOXYRIBOSE RESIDUES. THE
REMARK 3 FIRST 20 STRUCTURES WERE GENERATED FROM B-FORM DNA STARTING
REMARK 3 COORDINATES, AND THE
REMARK 3 SECOND 20 STRUCTURES WERE GENERATED FROM A-FORM DNA
REMARK 3 STARTING COORDINATES.
REMARK 4
REMARK 4 108D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000170020.
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 : MOLECULAR DYNAMICS, MATRIX
REMARK 210 RELAXATION
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 40
REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL
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: 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: 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 18 DG B 6 O4' DG B 6 C4' -0.062
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 1 DA A 5 O4' - C4' - C3' ANGL. DEV. = 3.9 DEGREES
REMARK 500 1 DA A 5 C4' - C3' - C2' ANGL. DEV. = -4.8 DEGREES
REMARK 500 1 DA A 5 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES
REMARK 500 1 DG A 6 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES
REMARK 500 1 DC A 7 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES
REMARK 500 1 DC B 3 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 1 DA B 5 O4' - C4' - C3' ANGL. DEV. = 4.8 DEGREES
REMARK 500 1 DA B 5 C4' - C3' - C2' ANGL. DEV. = -6.9 DEGREES
REMARK 500 1 DA B 5 O4' - C1' - C2' ANGL. DEV. = -5.8 DEGREES
REMARK 500 1 DA B 5 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES
REMARK 500 1 DC B 7 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 DG B 8 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES
REMARK 500 2 DC A 7 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES
REMARK 500 2 DC A 7 O4' - C1' - N1 ANGL. DEV. = 8.2 DEGREES
REMARK 500 2 DC B 3 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 2 DA B 5 O4' - C4' - C3' ANGL. DEV. = 5.2 DEGREES
REMARK 500 2 DA B 5 C4' - C3' - C2' ANGL. DEV. = -7.1 DEGREES
REMARK 500 2 DA B 5 C3' - C2' - C1' ANGL. DEV. = 7.6 DEGREES
REMARK 500 2 DA B 5 O4' - C1' - C2' ANGL. DEV. = -5.6 DEGREES
REMARK 500 2 DA B 5 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES
REMARK 500 2 DC B 7 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES
REMARK 500 3 DA A 5 O4' - C4' - C3' ANGL. DEV. = 4.2 DEGREES
REMARK 500 3 DC A 7 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES
REMARK 500 3 DC B 3 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 3 DA B 5 O4' - C4' - C3' ANGL. DEV. = 5.5 DEGREES
REMARK 500 3 DA B 5 C4' - C3' - C2' ANGL. DEV. = -7.3 DEGREES
REMARK 500 3 DA B 5 C3' - C2' - C1' ANGL. DEV. = 7.9 DEGREES
REMARK 500 3 DA B 5 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES
REMARK 500 3 DA B 5 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 3 DG B 6 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES
REMARK 500 3 DC B 7 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES
REMARK 500 4 DA A 5 O4' - C4' - C3' ANGL. DEV. = 4.3 DEGREES
REMARK 500 4 DC A 7 O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES
REMARK 500 4 DC A 7 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES
REMARK 500 4 DC B 3 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES
REMARK 500 4 DA B 5 O4' - C4' - C3' ANGL. DEV. = 5.5 DEGREES
REMARK 500 4 DA B 5 C4' - C3' - C2' ANGL. DEV. = -7.3 DEGREES
REMARK 500 4 DA B 5 C3' - C2' - C1' ANGL. DEV. = 7.9 DEGREES
REMARK 500 4 DA B 5 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES
REMARK 500 4 DA B 5 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 4 DG B 6 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES
REMARK 500 4 DC B 7 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES
REMARK 500 5 DA A 5 O4' - C4' - C3' ANGL. DEV. = 4.4 DEGREES
REMARK 500 5 DC A 7 O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES
REMARK 500 5 DC A 7 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES
REMARK 500 5 DC B 3 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 5 DA B 5 O4' - C4' - C3' ANGL. DEV. = 5.7 DEGREES
REMARK 500 5 DA B 5 C4' - C3' - C2' ANGL. DEV. = -7.4 DEGREES
REMARK 500 5 DA B 5 C3' - C2' - C1' ANGL. DEV. = 8.1 DEGREES
REMARK 500 5 DA B 5 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 383 ANGLE DEVIATIONS.
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 1 DC A 1 0.07 SIDE CHAIN
REMARK 500 1 DG A 2 0.06 SIDE CHAIN
REMARK 500 1 DT A 4 0.09 SIDE CHAIN
REMARK 500 1 DA A 5 0.08 SIDE CHAIN
REMARK 500 1 DT B 4 0.08 SIDE CHAIN
REMARK 500 2 DA A 5 0.06 SIDE CHAIN
REMARK 500 2 DT B 4 0.11 SIDE CHAIN
REMARK 500 2 DA B 5 0.06 SIDE CHAIN
REMARK 500 3 DA A 5 0.07 SIDE CHAIN
REMARK 500 3 DT B 4 0.11 SIDE CHAIN
REMARK 500 3 DA B 5 0.06 SIDE CHAIN
REMARK 500 4 DA A 5 0.08 SIDE CHAIN
REMARK 500 4 DC A 7 0.08 SIDE CHAIN
REMARK 500 4 DT B 4 0.11 SIDE CHAIN
REMARK 500 4 DA B 5 0.05 SIDE CHAIN
REMARK 500 5 DA A 5 0.08 SIDE CHAIN
REMARK 500 5 DC A 7 0.08 SIDE CHAIN
REMARK 500 5 DT B 4 0.10 SIDE CHAIN
REMARK 500 5 DA B 5 0.08 SIDE CHAIN
REMARK 500 5 DC B 7 0.08 SIDE CHAIN
REMARK 500 6 DC A 1 0.07 SIDE CHAIN
REMARK 500 6 DG A 2 0.09 SIDE CHAIN
REMARK 500 6 DA A 5 0.09 SIDE CHAIN
REMARK 500 6 DC A 7 0.08 SIDE CHAIN
REMARK 500 6 DT B 4 0.07 SIDE CHAIN
REMARK 500 6 DA B 5 0.13 SIDE CHAIN
REMARK 500 7 DC A 1 0.07 SIDE CHAIN
REMARK 500 7 DG A 2 0.09 SIDE CHAIN
REMARK 500 7 DA A 5 0.09 SIDE CHAIN
REMARK 500 7 DC A 7 0.07 SIDE CHAIN
REMARK 500 7 DT B 4 0.08 SIDE CHAIN
REMARK 500 7 DA B 5 0.13 SIDE CHAIN
REMARK 500 7 DC B 7 0.08 SIDE CHAIN
REMARK 500 8 DC A 1 0.07 SIDE CHAIN
REMARK 500 8 DG A 2 0.08 SIDE CHAIN
REMARK 500 8 DT A 4 0.08 SIDE CHAIN
REMARK 500 8 DA A 5 0.07 SIDE CHAIN
REMARK 500 8 DT B 4 0.08 SIDE CHAIN
REMARK 500 8 DA B 5 0.06 SIDE CHAIN
REMARK 500 8 DC B 7 0.09 SIDE CHAIN
REMARK 500 9 DC A 1 0.07 SIDE CHAIN
REMARK 500 9 DG A 2 0.08 SIDE CHAIN
REMARK 500 9 DA A 5 0.07 SIDE CHAIN
REMARK 500 9 DT B 4 0.09 SIDE CHAIN
REMARK 500 9 DA B 5 0.06 SIDE CHAIN
REMARK 500 9 DG B 6 0.08 SIDE CHAIN
REMARK 500 9 DC B 7 0.07 SIDE CHAIN
REMARK 500 10 DC A 1 0.07 SIDE CHAIN
REMARK 500 10 DG A 2 0.09 SIDE CHAIN
REMARK 500 10 DA A 5 0.08 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 207 PLANE DEVIATIONS.
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 TOT A 9
DBREF 108D A 1 8 PDB 108D 108D 1 8
DBREF 108D B 1 8 PDB 108D 108D 1 8
SEQRES 1 A 8 DC DG DC DT DA DG DC DG
SEQRES 1 B 8 DC DG DC DT DA DG DC DG
HET TOT A 9 115
HETNAM TOT 1,1-(4,4,8,8-TETRAMETHYL-4,8-DIAZAUNDECAMETHYLENE)-BIS-
HETNAM 2 TOT 4-3-METHYL-2,3-DIHYDRO-(BENZO-1,3-THIAZOLE)-2-
HETNAM 3 TOT METHYLIDENE)-QUINOLINIUM
FORMUL 3 TOT C49 H58 N6 S2 4+
SITE 1 AC1 8 DC A 3 DT A 4 DA A 5 DG A 6
SITE 2 AC1 8 DC B 3 DT B 4 DA B 5 DG B 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
MODEL 1
Complete list - b 16 2 Bytes