Header list of 148d.pdb file
Complete list - 16 20 Bytes
HEADER DNA 15-NOV-93 148D
TITLE THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE THROMBIN BINDING DNA
TITLE 2 APTAMER D(GGTTGGTGTGGTTGG)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-
COMPND 3 3');
COMPND 4 CHAIN: A;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED
KEYWDS DNA
EXPDTA SOLUTION NMR
NUMMDL 12
AUTHOR P.SCHULTZE,R.F.MACAYA,J.FEIGON
REVDAT 5 16-FEB-22 148D 1 REMARK
REVDAT 4 07-APR-09 148D 1 REMARK
REVDAT 3 24-FEB-09 148D 1 VERSN
REVDAT 2 01-APR-03 148D 1 JRNL
REVDAT 1 30-APR-94 148D 0
JRNL AUTH P.SCHULTZE,R.F.MACAYA,J.FEIGON
JRNL TITL THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE THROMBIN-BINDING
JRNL TITL 2 DNA APTAMER D(GGTTGGTGTGGTTGG).
JRNL REF J.MOL.BIOL. V. 235 1532 1994
JRNL REFN ISSN 0022-2836
JRNL PMID 8107090
JRNL DOI 10.1006/JMBI.1994.1105
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH R.F.MACAYA,P.SCHULTZE,F.W.SMITH,J.A.ROE,J.FEIGON
REMARK 1 TITL THROMBIN-BINDING DNA APTAMER FORMS A UNIMOLECULAR QUADRUPLEX
REMARK 1 TITL 2 STRUCTURE IN SOLUTION
REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 90 3745 1993
REMARK 1 REFN ISSN 0027-8424
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR
REMARK 3 AUTHORS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: STEP (1) SUBSTRUCTURE EMBEDDING ON 20
REMARK 3 STRUCTURES STEP (2) TEMPLATE FITTING AND REGULARIZATION BY
REMARK 3 SIMULATED ANNEALING (20 STRUCTURES) STEP (3) SIMULATED ANNEALING
REMARK 3 AND ENERGY MINIMIZATION (20 STRUCTURES) STEP (4) RELAXATION
REMARK 3 MATRIX REFINEMENT ON THE BEST 6 OF 20 STRUCTURES THIS PROCEDURE
REMARK 3 WAS CARRIED OUT SEPARATELY WITH DISTANCE RESTRAINTS ENFORCING
REMARK 3 HYDROGEN BONDING BETWEEN T4 AND T13 INVOLVING O2 ATOMS IN ONE
REMARK 3 CASE (MODELS 1-6) AND O4 ATOMS IN THE OTHER (MODELS 7-12). ALL
REMARK 3 MODELS WERE SUPERIMPOSED ON MODEL 1, USING ALL NON-HYDROGEN
REMARK 3 ATOMS OF G1, G2, G5, G6, G10, G11, G14, G15; I.E., ALL G
REMARK 3 RESIDUES PARTICIPATING IN TETRAD FORMATION.
REMARK 4
REMARK 4 148D 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_1000170109.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : NULL
REMARK 210 PH : 6.1
REMARK 210 IONIC STRENGTH : 0.11M
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 : SIMULATED ANNEALING, MATRIX
REMARK 210 RELAXATION
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 20
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 12
REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
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 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 DT A 4 C5 DT A 4 C7 0.041
REMARK 500 1 DT A 7 C5 DT A 7 C7 0.047
REMARK 500 1 DG A 8 C5' DG A 8 C4' 0.050
REMARK 500 1 DT A 9 C5' DT A 9 C4' 0.119
REMARK 500 1 DT A 9 C5 DT A 9 C7 0.048
REMARK 500 1 DG A 10 C5' DG A 10 C4' 0.054
REMARK 500 1 DT A 12 C5 DT A 12 C7 0.038
REMARK 500 2 DT A 3 C5 DT A 3 C7 0.037
REMARK 500 2 DT A 4 C5 DT A 4 C7 0.042
REMARK 500 2 DG A 5 C8 DG A 5 N9 -0.043
REMARK 500 2 DT A 7 C5 DT A 7 C7 0.045
REMARK 500 2 DG A 8 C5' DG A 8 C4' 0.061
REMARK 500 2 DT A 9 C5' DT A 9 C4' 0.129
REMARK 500 2 DT A 12 C5 DT A 12 C7 0.038
REMARK 500 3 DT A 4 C5 DT A 4 C7 0.040
REMARK 500 3 DT A 7 C5 DT A 7 C7 0.043
REMARK 500 3 DG A 8 C5' DG A 8 C4' 0.051
REMARK 500 3 DT A 9 C5' DT A 9 C4' 0.121
REMARK 500 3 DT A 9 C5 DT A 9 C7 0.041
REMARK 500 3 DT A 12 C5 DT A 12 C7 0.039
REMARK 500 4 DT A 3 C5 DT A 3 C7 0.040
REMARK 500 4 DT A 4 C5' DT A 4 C4' 0.043
REMARK 500 4 DG A 5 C5' DG A 5 C4' 0.047
REMARK 500 4 DT A 7 C5 DT A 7 C7 0.041
REMARK 500 4 DG A 8 C5' DG A 8 C4' 0.061
REMARK 500 4 DT A 9 C5' DT A 9 C4' 0.134
REMARK 500 4 DT A 12 C5 DT A 12 C7 0.038
REMARK 500 5 DT A 3 C5 DT A 3 C7 0.036
REMARK 500 5 DT A 4 C5 DT A 4 C7 0.036
REMARK 500 5 DG A 6 C2' DG A 6 C1' -0.063
REMARK 500 5 DG A 6 C8 DG A 6 N9 -0.048
REMARK 500 5 DT A 7 C5 DT A 7 C7 0.039
REMARK 500 5 DG A 8 C5' DG A 8 C4' 0.058
REMARK 500 5 DT A 9 C5' DT A 9 C4' 0.085
REMARK 500 5 DT A 9 C5 DT A 9 C7 0.039
REMARK 500 5 DG A 10 C5' DG A 10 C4' 0.057
REMARK 500 5 DT A 12 C5 DT A 12 C7 0.039
REMARK 500 6 DT A 3 C5 DT A 3 C7 0.038
REMARK 500 6 DG A 6 C8 DG A 6 N9 -0.046
REMARK 500 6 DT A 7 C5 DT A 7 C7 0.042
REMARK 500 6 DG A 8 C5' DG A 8 C4' 0.042
REMARK 500 6 DT A 9 C5' DT A 9 C4' 0.077
REMARK 500 6 DT A 9 C5 DT A 9 C7 0.039
REMARK 500 6 DG A 10 C5' DG A 10 C4' 0.060
REMARK 500 6 DT A 12 C5 DT A 12 C7 0.039
REMARK 500 7 DT A 3 C5 DT A 3 C7 0.036
REMARK 500 7 DT A 4 C5 DT A 4 C7 0.042
REMARK 500 7 DT A 7 C5 DT A 7 C7 0.042
REMARK 500 7 DG A 8 C5' DG A 8 C4' 0.058
REMARK 500 7 DT A 9 C5' DT A 9 C4' 0.115
REMARK 500
REMARK 500 THIS ENTRY HAS 84 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 1 O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES
REMARK 500 1 DG A 1 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES
REMARK 500 1 DG A 2 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES
REMARK 500 1 DT A 3 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 1 DT A 3 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES
REMARK 500 1 DT A 4 C5' - C4' - O4' ANGL. DEV. = 6.8 DEGREES
REMARK 500 1 DT A 4 O4' - C1' - C2' ANGL. DEV. = -6.2 DEGREES
REMARK 500 1 DG A 5 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES
REMARK 500 1 DG A 5 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 1 DG A 6 C4' - C3' - C2' ANGL. DEV. = -6.5 DEGREES
REMARK 500 1 DG A 6 O4' - C1' - C2' ANGL. DEV. = -7.3 DEGREES
REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 1 DG A 6 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES
REMARK 500 1 DT A 7 O3' - P - O5' ANGL. DEV. = -16.7 DEGREES
REMARK 500 1 DT A 7 O4' - C4' - C3' ANGL. DEV. = 4.2 DEGREES
REMARK 500 1 DT A 7 C4' - C3' - C2' ANGL. DEV. = -5.0 DEGREES
REMARK 500 1 DG A 8 C5' - C4' - O4' ANGL. DEV. = 12.8 DEGREES
REMARK 500 1 DG A 8 C4' - C3' - C2' ANGL. DEV. = -4.9 DEGREES
REMARK 500 1 DG A 8 C3' - C2' - C1' ANGL. DEV. = 7.6 DEGREES
REMARK 500 1 DG A 8 O4' - C1' - C2' ANGL. DEV. = -6.8 DEGREES
REMARK 500 1 DG A 8 N9 - C1' - C2' ANGL. DEV. = -12.9 DEGREES
REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = -4.8 DEGREES
REMARK 500 1 DG A 8 C5 - N7 - C8 ANGL. DEV. = -3.4 DEGREES
REMARK 500 1 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 1 DT A 9 P - O5' - C5' ANGL. DEV. = 9.7 DEGREES
REMARK 500 1 DT A 9 O4' - C4' - C3' ANGL. DEV. = -4.2 DEGREES
REMARK 500 1 DT A 9 C1' - O4' - C4' ANGL. DEV. = 4.6 DEGREES
REMARK 500 1 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES
REMARK 500 1 DT A 9 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES
REMARK 500 1 DG A 11 C5 - N7 - C8 ANGL. DEV. = -3.2 DEGREES
REMARK 500 1 DG A 11 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 1 DT A 12 O4' - C1' - N1 ANGL. DEV. = 7.0 DEGREES
REMARK 500 1 DT A 13 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES
REMARK 500 1 DG A 15 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 1 DG A 15 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 1 DG A 15 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES
REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES
REMARK 500 2 DG A 1 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES
REMARK 500 2 DG A 2 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 2 DT A 3 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 2 DT A 3 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES
REMARK 500 2 DT A 4 C5' - C4' - O4' ANGL. DEV. = 10.3 DEGREES
REMARK 500 2 DT A 4 O4' - C1' - C2' ANGL. DEV. = -7.1 DEGREES
REMARK 500 2 DG A 5 O4' - C4' - C3' ANGL. DEV. = -3.5 DEGREES
REMARK 500 2 DG A 5 C5' - C4' - C3' ANGL. DEV. = 7.4 DEGREES
REMARK 500 2 DG A 5 O4' - C1' - N9 ANGL. DEV. = -5.3 DEGREES
REMARK 500 2 DG A 5 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 2 DG A 6 C5' - C4' - O4' ANGL. DEV. = 7.7 DEGREES
REMARK 500 2 DG A 6 O4' - C1' - C2' ANGL. DEV. = -5.9 DEGREES
REMARK 500 2 DG A 6 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 402 ANGLE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
DBREF 148D A 1 15 PDB 148D 148D 1 15
SEQRES 1 A 15 DG DG DT DT DG DG DT DG DT DG DG DT DT
SEQRES 2 A 15 DG DG
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