Header list of 177d.pdb file
Complete list - 16 20 Bytes
HEADER DNA 24-MAY-94 177D
TITLE SOLUTION STRUCTURE AND HYDRATION PATTERNS OF A PYRIMIDINE(DOT)
TITLE 2 PURINE(DOT)PYRIMIDINE DNA TRIPLEX CONTAINING A NOVEL T(DOT)CG TRIPLE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-
COMPND 3 D(*GP*AP*AP*CP*AP*GP*GP*TP*TP*TP*TP*T*CP*CP*TP*GP*TP*TP*CP*TP*TP*TP*T
COMPND 4 P*T*CP*TP*TP*TP*TP*CP*C)-3');
COMPND 5 CHAIN: A;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED
KEYWDS DNA, TRIPLEX
EXPDTA SOLUTION NMR
NUMMDL 6
AUTHOR I.RADHAKRISHNAN,D.J.PATEL
REVDAT 4 16-FEB-22 177D 1 REMARK
REVDAT 3 24-FEB-09 177D 1 VERSN
REVDAT 2 01-APR-03 177D 1 JRNL
REVDAT 1 15-OCT-94 177D 0
JRNL AUTH I.RADHAKRISHNAN,D.J.PATEL
JRNL TITL SOLUTION STRUCTURE AND HYDRATION PATTERNS OF A
JRNL TITL 2 PYRIMIDINE.PURINE.PYRIMIDINE DNA TRIPLEX CONTAINING A NOVEL
JRNL TITL 3 T.CG BASE-TRIPLE.
JRNL REF J.MOL.BIOL. V. 241 600 1994
JRNL REFN ISSN 0022-2836
JRNL PMID 8057381
JRNL DOI 10.1006/JMBI.1994.1534
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: NUMBER OF NUCLEIC ACID ATOMS -- 415
REMARK 3 RESTRAINED MOLECULAR DYNAMICS CALCULATIONS WERE CONDUCTED ON
REMARK 3 IDEALIZED A'- AND B-FORM STARTING STRUCTURES. ONLY THE TRIPLEX
REMARK 3 REGION IN THE SEQUENCE WAS CONSIDERED. SIX STRUCTURES WERE
REMARK 3 CALCULATED INITIALLY USING DISTANCE RESTRAINTS. A MAJORITY OF
REMARK 3 THE DISTANCE RESTRAINTS WERE SUBSEQUENTLY REPLACED BY NOE
REMARK 3 INTENSITY RESTRAINTS. THE R(1/6) VALUE WAS MONITORED DURING THE
REMARK 3 REFINEMENTS. EACH STRUCTURE WAS SUBJECTED TO 500 CYCLES OF
REMARK 3 ENERGY MINIMIZATION AFTER THE DYNAMICS. NO AVERAGE STRUCTURE WAS
REMARK 3 CALCULATED. THE R(1/6) VALUE FOR THE MINIMIZED STRUCTURE
REMARK 3 REPRESENTING THE ENSEMBLE IS 0.024. THE DYNAMICS SIMULATIONS
REMARK 3 WERE PERFORMED IN THE PRESENCE OF EXPLICIT SOLVENT MOLECULES AND
REMARK 3 15 NA+ COUNTER IONS. THE SUMMATION EXTENDS THROUGH ALL
REMARK 3 ASSIGNABLE, QUANTIFIABLE CROSS PEAK INTENSITIES IN NOESY SPECTRA
REMARK 3 RECORDED AT MIXING TIMES OF 40, 90 AND 150 MS. RMS DEVIATIONS
REMARK 3 FROM IDEALIZED GEOMETRY FOR THE MINIMIZED STRUCTURE `RM'
REMARK 3 REPRESENTING THE ENSEMBLE ARE AS FOLLOWS: RM BOND (ANGSTROMS)
REMARK 3 0.016 (0.016) ANGLES (DEGREES) 3.825 (3.734) IMPROPERS (DEGREES)
REMARK 3 0.552 (0.391) THE VALUES IN PARENTHESES CORRESPOND TO THE
REMARK 3 AVERAGE VALUES FOR THE ENSEMBLE OF SIX STRUCTURES.
REMARK 4
REMARK 4 177D 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_1000170171.
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, DISTANCE
REMARK 210 GEOMETRY
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 6
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 6
REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES
REMARK 210 SUBMITTED
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 MODELS 1-6
REMARK 465 RES C SSSEQI
REMARK 465 DT A -15
REMARK 465 DT A -16
REMARK 465 DT A -17
REMARK 465 DT A -18
REMARK 465 DT A 0
REMARK 465 DT A -10
REMARK 465 DT A -11
REMARK 465 DT A -12
REMARK 465 DT A -13
REMARK 465 DT A -14
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 MODELS 1-6
REMARK 470 RES CSSEQI ATOMS
REMARK 470 DC A 1 P OP1 OP2
REMARK 470 DC A 15 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 1 DG A 8 N1 DG A 8 C2 -0.095
REMARK 500 1 DG A 8 C4 DG A 8 C5 0.085
REMARK 500 1 DG A 8 N7 DG A 8 C8 0.064
REMARK 500 1 DA A 9 C4 DA A 9 C5 0.075
REMARK 500 1 DA A 9 C6 DA A 9 N1 -0.042
REMARK 500 1 DA A 9 N7 DA A 9 C8 0.044
REMARK 500 1 DA A 10 C4 DA A 10 C5 0.071
REMARK 500 1 DA A 10 N7 DA A 10 C8 0.045
REMARK 500 1 DC A 11 C5' DC A 11 C4' 0.049
REMARK 500 1 DC A 11 N1 DC A 11 C6 -0.046
REMARK 500 1 DC A 11 N3 DC A 11 C4 -0.057
REMARK 500 1 DC A 11 C4 DC A 11 C5 -0.064
REMARK 500 1 DA A 12 C4 DA A 12 C5 0.072
REMARK 500 1 DG A 13 N1 DG A 13 C2 -0.093
REMARK 500 1 DG A 13 C4 DG A 13 C5 0.089
REMARK 500 1 DG A 13 N7 DG A 13 C8 0.075
REMARK 500 1 DG A 14 N1 DG A 14 C2 -0.097
REMARK 500 1 DG A 14 C4 DG A 14 C5 0.092
REMARK 500 1 DG A 14 N7 DG A 14 C8 0.056
REMARK 500 1 DC A 1 N3 DC A 1 C4 -0.062
REMARK 500 1 DC A 1 C4 DC A 1 C5 -0.056
REMARK 500 1 DC A 1 C5 DC A 1 C6 0.050
REMARK 500 1 DC A 2 N1 DC A 2 C6 -0.053
REMARK 500 1 DC A 2 N3 DC A 2 C4 -0.059
REMARK 500 1 DC A 2 C4 DC A 2 C5 -0.051
REMARK 500 1 DT A 3 C2 DT A 3 N3 -0.085
REMARK 500 1 DT A 3 N3 DT A 3 C4 -0.080
REMARK 500 1 DT A 3 C4 DT A 3 C5 0.081
REMARK 500 1 DT A 3 C5 DT A 3 C6 0.051
REMARK 500 1 DT A 3 C6 DT A 3 N1 -0.051
REMARK 500 1 DG A 4 N1 DG A 4 C2 -0.106
REMARK 500 1 DG A 4 C4 DG A 4 C5 0.089
REMARK 500 1 DG A 4 N7 DG A 4 C8 0.046
REMARK 500 1 DG A 4 C8 DG A 4 N9 -0.046
REMARK 500 1 DT A 5 C2 DT A 5 N3 -0.078
REMARK 500 1 DT A 5 N3 DT A 5 C4 -0.074
REMARK 500 1 DT A 5 C4 DT A 5 C5 0.077
REMARK 500 1 DT A 5 C5 DT A 5 C6 0.045
REMARK 500 1 DT A 5 C6 DT A 5 N1 -0.045
REMARK 500 1 DT A 6 C2 DT A 6 N3 -0.076
REMARK 500 1 DT A 6 N3 DT A 6 C4 -0.077
REMARK 500 1 DT A 6 C4 DT A 6 C5 0.087
REMARK 500 1 DT A 6 C5 DT A 6 C6 0.056
REMARK 500 1 DT A 6 C6 DT A 6 N1 -0.046
REMARK 500 1 DC A 7 N1 DC A 7 C6 -0.042
REMARK 500 1 DC A 7 N3 DC A 7 C4 -0.068
REMARK 500 1 DC A 7 C4 DC A 7 C5 -0.066
REMARK 500 1 DC A 7 C5 DC A 7 C6 0.059
REMARK 500 1 DC A 15 N3 DC A 15 C4 -0.073
REMARK 500 1 DC A 15 C5 DC A 15 C6 0.060
REMARK 500
REMARK 500 THIS ENTRY HAS 460 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 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 1 DG A 8 C2 - N3 - C4 ANGL. DEV. = 5.4 DEGREES
REMARK 500 1 DG A 8 N3 - C4 - C5 ANGL. DEV. = -7.3 DEGREES
REMARK 500 1 DG A 8 C5 - C6 - N1 ANGL. DEV. = 5.1 DEGREES
REMARK 500 1 DG A 8 N3 - C4 - N9 ANGL. DEV. = 7.0 DEGREES
REMARK 500 1 DG A 8 C6 - C5 - N7 ANGL. DEV. = 4.4 DEGREES
REMARK 500 1 DG A 8 N3 - C2 - N2 ANGL. DEV. = -4.8 DEGREES
REMARK 500 1 DG A 8 N1 - C6 - O6 ANGL. DEV. = -3.6 DEGREES
REMARK 500 1 DA A 9 O3' - P - O5' ANGL. DEV. = 11.4 DEGREES
REMARK 500 1 DA A 9 OP1 - P - OP2 ANGL. DEV. = -11.1 DEGREES
REMARK 500 1 DA A 9 N1 - C2 - N3 ANGL. DEV. = -4.0 DEGREES
REMARK 500 1 DA A 9 C2 - N3 - C4 ANGL. DEV. = 6.5 DEGREES
REMARK 500 1 DA A 9 C4 - C5 - C6 ANGL. DEV. = -6.0 DEGREES
REMARK 500 1 DA A 9 C5 - C6 - N1 ANGL. DEV. = 8.0 DEGREES
REMARK 500 1 DA A 9 C6 - C5 - N7 ANGL. DEV. = 7.3 DEGREES
REMARK 500 1 DA A 9 N1 - C6 - N6 ANGL. DEV. = -9.6 DEGREES
REMARK 500 1 DA A 10 O3' - P - O5' ANGL. DEV. = 13.7 DEGREES
REMARK 500 1 DA A 10 OP1 - P - OP2 ANGL. DEV. = -11.9 DEGREES
REMARK 500 1 DA A 10 O4' - C1' - N9 ANGL. DEV. = -8.3 DEGREES
REMARK 500 1 DA A 10 C2 - N3 - C4 ANGL. DEV. = 7.5 DEGREES
REMARK 500 1 DA A 10 N3 - C4 - C5 ANGL. DEV. = -5.4 DEGREES
REMARK 500 1 DA A 10 C4 - C5 - C6 ANGL. DEV. = -4.1 DEGREES
REMARK 500 1 DA A 10 C5 - C6 - N1 ANGL. DEV. = 7.7 DEGREES
REMARK 500 1 DA A 10 C6 - C5 - N7 ANGL. DEV. = 7.0 DEGREES
REMARK 500 1 DA A 10 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES
REMARK 500 1 DC A 11 O3' - P - O5' ANGL. DEV. = 12.6 DEGREES
REMARK 500 1 DC A 11 OP1 - P - OP2 ANGL. DEV. = -11.0 DEGREES
REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 1 DC A 11 N3 - C4 - C5 ANGL. DEV. = 2.6 DEGREES
REMARK 500 1 DC A 11 N1 - C2 - O2 ANGL. DEV. = 7.0 DEGREES
REMARK 500 1 DC A 11 N3 - C2 - O2 ANGL. DEV. = -5.5 DEGREES
REMARK 500 1 DA A 12 O3' - P - O5' ANGL. DEV. = 14.3 DEGREES
REMARK 500 1 DA A 12 OP1 - P - OP2 ANGL. DEV. = -10.8 DEGREES
REMARK 500 1 DA A 12 N1 - C2 - N3 ANGL. DEV. = -4.0 DEGREES
REMARK 500 1 DA A 12 C2 - N3 - C4 ANGL. DEV. = 7.1 DEGREES
REMARK 500 1 DA A 12 N3 - C4 - C5 ANGL. DEV. = -4.5 DEGREES
REMARK 500 1 DA A 12 C4 - C5 - C6 ANGL. DEV. = -4.6 DEGREES
REMARK 500 1 DA A 12 C5 - C6 - N1 ANGL. DEV. = 7.5 DEGREES
REMARK 500 1 DA A 12 N3 - C4 - N9 ANGL. DEV. = 4.8 DEGREES
REMARK 500 1 DA A 12 C6 - C5 - N7 ANGL. DEV. = 6.2 DEGREES
REMARK 500 1 DA A 12 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES
REMARK 500 1 DG A 13 O3' - P - O5' ANGL. DEV. = 12.0 DEGREES
REMARK 500 1 DG A 13 OP1 - P - OP2 ANGL. DEV. = -10.7 DEGREES
REMARK 500 1 DG A 13 C2 - N3 - C4 ANGL. DEV. = 5.1 DEGREES
REMARK 500 1 DG A 13 N3 - C4 - C5 ANGL. DEV. = -7.0 DEGREES
REMARK 500 1 DG A 13 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES
REMARK 500 1 DG A 13 N3 - C4 - N9 ANGL. DEV. = 5.9 DEGREES
REMARK 500 1 DG A 13 C6 - C5 - N7 ANGL. DEV. = 4.9 DEGREES
REMARK 500 1 DG A 13 N3 - C2 - N2 ANGL. DEV. = -6.0 DEGREES
REMARK 500 1 DG A 14 O3' - P - O5' ANGL. DEV. = 11.6 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 789 ANGLE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
DBREF 177D A 8 21 PDB 177D 177D 8 21
SEQRES 1 A 31 DG DA DA DC DA DG DG DT DT DT DT DT DC
SEQRES 2 A 31 DC DT DG DT DT DC DT DT DT DT DT DC DT
SEQRES 3 A 31 DT DT DT DC DC
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 - 16 20 Bytes