Header list of 135d.pdb file
Complete list - 16 202 Bytes
HEADER DNA 30-AUG-93 135D
TITLE SOLUTION STRUCTURE OF A PURINE(DOT)PURINE(DOT)PYRIMIDINE DNA TRIPLEX
TITLE 2 CONTAINING G(DOT)GC AND T(DOT)AT TRIPLES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA TRIPLEX;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED
KEYWDS DNA, TRIPLEX
EXPDTA SOLUTION NMR
AUTHOR I.RADHAKRISHNAN,D.J.PATEL
REVDAT 4 16-FEB-22 135D 1 REMARK
REVDAT 3 24-FEB-09 135D 1 VERSN
REVDAT 2 01-APR-03 135D 1 JRNL
REVDAT 1 30-APR-94 135D 0
JRNL AUTH I.RADHAKRISHNAN,D.J.PATEL
JRNL TITL SOLUTION STRUCTURE OF A PURINE.PURINE.PYRIMIDINE DNA TRIPLEX
JRNL TITL 2 CONTAINING G.GC AND T.AT TRIPLES.
JRNL REF STRUCTURE V. 1 135 1993
JRNL REFN ISSN 0969-2126
JRNL PMID 8069626
JRNL DOI 10.1016/0969-2126(93)90028-F
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH I.RADHAKRISHNAN,D.J.PATEL
REMARK 1 TITL SOLUTION STRUCTURE OF AN INTRAMOLECULAR
REMARK 1 TITL 2 PURINE(DOT)PURINE(DOT)PYRIMIDINE DNA TRIPLEX
REMARK 1 REF J.AM.CHEM.SOC. V. 115 1615 1993
REMARK 1 REFN ISSN 0002-7863
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: RESTRAINED MOLECULAR DYNAMICS
REMARK 3 CALCULATIONS WERE DONE ONIDEALIZED A'- AND B-FORM STARTING
REMARK 3 STRUCTURES. ONLY THE TRIPLEX REGION AND THE FIRST AND LAST
REMARK 3 RESIDUES OF EACH OF THE TWO LOOPS IN THE SEQUENCE WERE
REMARK 3 CONSIDERED. THE REFINEMENT WAS CONDUCTED IN TWO STAGES. IN THE
REMARK 3 FIRST STAGE, SIX STRUCTURES WERE CALCULATED (THREE FROM EACH
REMARK 3 STARTING STRUCTURE) USING DISTANCE RESTRAINTS. IN THE SECOND
REMARK 3 STAGE, TWO OF THE SIX STRUCTURES WERE REFINED DIRECTLY AGAINST
REMARK 3 PRIMARY NOE DATA. THE R(1/6) VALUE WAS USED TO MONITOR THE
REMARK 3 REFINEMENT DURING THIS STAGE. THE FINAL R(1/6) VALUES FOR THE
REMARK 3 TWO AVERAGED MINIMIZED STRUCTURES WERE 0.04 AND 0.045.
REMARK 4
REMARK 4 135D 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_1000170083.
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 : RESTRAINED MOLECULAR DYNAMICS,
REMARK 210 DISTANCE GEOMETRY
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL
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: 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: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
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 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465 RES C SSSEQI
REMARK 465 DT A 2L
REMARK 465 DT A 3L
REMARK 465 DT A 4L
REMARK 465 DT A 7L
REMARK 465 DT A 8L
REMARK 465 DT A 9L
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 DT A 5L P OP1 OP2
REMARK 470 DT A 10L P OP1 OP2
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 DT A 1 C3' DT A 1 C2' 0.078
REMARK 500 DT A 1 C2' DT A 1 C1' 0.063
REMARK 500 DT A 1 C5 DT A 1 C7 0.038
REMARK 500 DC A 2 N1 DC A 2 C6 0.040
REMARK 500 DC A 3 N1 DC A 3 C6 0.037
REMARK 500 DT A 4 C5 DT A 4 C7 0.042
REMARK 500 DC A 5 N1 DC A 5 C6 0.047
REMARK 500 DT A 7 C5 DT A 7 C7 0.050
REMARK 500 DT A 5L C5 DT A 5L C7 0.042
REMARK 500 DA A 8 C2' DA A 8 C1' 0.065
REMARK 500 DG A 9 C4' DG A 9 C3' 0.117
REMARK 500 DG A 9 C3' DG A 9 C2' 0.124
REMARK 500 DG A 9 C2' DG A 9 C1' 0.063
REMARK 500 DA A 11 C4' DA A 11 C3' 0.061
REMARK 500 DA A 11 C3' DA A 11 C2' 0.100
REMARK 500 DT A 6L C3' DT A 6L C2' 0.082
REMARK 500 DT A 6L C2' DT A 6L C1' 0.102
REMARK 500 DT A 15 C3' DT A 15 C2' 0.123
REMARK 500 DT A 15 C2' DT A 15 C1' 0.063
REMARK 500 DG A 17 C2' DG A 17 C1' 0.083
REMARK 500 DT A 18 C3' DT A 18 C2' 0.128
REMARK 500 DT A 18 C2' DT A 18 C1' 0.111
REMARK 500 DT A 18 C5 DT A 18 C7 0.043
REMARK 500 DG A 19 C2' DG A 19 C1' 0.085
REMARK 500 DG A 20 C3' DG A 20 C2' 0.077
REMARK 500 DG A 20 C2' DG A 20 C1' 0.098
REMARK 500 DT A 21 C4' DT A 21 C3' 0.080
REMARK 500 DT A 21 C5 DT A 21 C7 0.041
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 DT A 1 O4' - C1' - C2' ANGL. DEV. = -5.9 DEGREES
REMARK 500 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 DC A 2 C4' - C3' - C2' ANGL. DEV. = -4.2 DEGREES
REMARK 500 DC A 2 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES
REMARK 500 DC A 2 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES
REMARK 500 DC A 2 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = -7.1 DEGREES
REMARK 500 DT A 4 C1' - O4' - C4' ANGL. DEV. = -7.6 DEGREES
REMARK 500 DT A 4 O4' - C1' - C2' ANGL. DEV. = -6.9 DEGREES
REMARK 500 DT A 4 O4' - C1' - N1 ANGL. DEV. = 8.5 DEGREES
REMARK 500 DT A 4 N3 - C2 - O2 ANGL. DEV. = -3.8 DEGREES
REMARK 500 DC A 5 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DT A 7 C1' - O4' - C4' ANGL. DEV. = -7.1 DEGREES
REMARK 500 DT A 7 O4' - C1' - C2' ANGL. DEV. = -6.4 DEGREES
REMARK 500 DT A 7 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 DT A 1L C6 - C5 - C7 ANGL. DEV. = -4.8 DEGREES
REMARK 500 DT A 5L C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES
REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 DG A 10 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES
REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 DA A 11 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 DG A 13 O4' - C1' - C2' ANGL. DEV. = -8.8 DEGREES
REMARK 500 DG A 13 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES
REMARK 500 DA A 14 O4' - C1' - N9 ANGL. DEV. = 6.9 DEGREES
REMARK 500 DT A 6L O4' - C1' - N1 ANGL. DEV. = -8.7 DEGREES
REMARK 500 DT A 6L C4 - C5 - C6 ANGL. DEV. = 4.1 DEGREES
REMARK 500 DT A 6L C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES
REMARK 500 DT A 10L C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES
REMARK 500 DT A 10L O4' - C1' - C2' ANGL. DEV. = -5.7 DEGREES
REMARK 500 DT A 10L O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 DT A 15 C1' - O4' - C4' ANGL. DEV. = -8.4 DEGREES
REMARK 500 DT A 15 C4' - C3' - C2' ANGL. DEV. = -8.5 DEGREES
REMARK 500 DT A 15 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES
REMARK 500 DT A 15 N1 - C2 - N3 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DT A 15 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES
REMARK 500 DG A 16 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES
REMARK 500 DG A 17 C1' - O4' - C4' ANGL. DEV. = 4.3 DEGREES
REMARK 500 DT A 18 C4' - C3' - C2' ANGL. DEV. = -4.5 DEGREES
REMARK 500 DT A 18 N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES
REMARK 500 DT A 18 C6 - C5 - C7 ANGL. DEV. = -5.8 DEGREES
REMARK 500 DG A 20 O3' - P - O5' ANGL. DEV. = -11.6 DEGREES
REMARK 500 DG A 20 C1' - O4' - C4' ANGL. DEV. = 5.6 DEGREES
REMARK 500 DT A 21 O4' - C4' - C3' ANGL. DEV. = -3.5 DEGREES
REMARK 500 DT A 21 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES
REMARK 500 DT A 21 C4' - C3' - C2' ANGL. DEV. = -5.2 DEGREES
REMARK 500 DT A 21 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 134D RELATED DB: PDB
REMARK 900 MINIMIZED AVERAGE STRUCTURE
REMARK 900 RELATED ID: 136D RELATED DB: PDB
REMARK 900 ENSEMBLE OF 14 STRUCTURES
DBREF 135D A 1 21 PDB 135D 135D 1 21
SEQRES 1 A 31 DT DC DC DT DC DC DT DT DT DT DT DT DA
SEQRES 2 A 31 DG DG DA DG DG DA DT DT DT DT DT DT DG
SEQRES 3 A 31 DG DT DG DG DT
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 - 16 202 Bytes