Header list of 1db6.pdb file
Complete list - 16 20 Bytes
HEADER DNA 02-NOV-99 1DB6
TITLE SOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGACCAACGTGTCGCCTGGTCG-3'
TITLE 2 COMPLEXED WITH ARGININAMIDE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: SEQUENCE IS DERIVED FROM IN-VITRO SELECTION
SOURCE 4 EXPERIMENTS. SEQUENCES WERE CHEMICALLY SYTHETHESIZED.
KEYWDS APTAMER, ARGININE, ARGININAMIDE, SINGLE-STRAND, HAIRPIN, SELEX, DNA
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR S.A.ROBERTSON,K.HARADA,A.D.FRANKEL,D.E.WEMMER
REVDAT 4 16-FEB-22 1DB6 1 REMARK
REVDAT 3 24-FEB-09 1DB6 1 VERSN
REVDAT 2 01-MAY-00 1DB6 1 REMARK ATOM
REVDAT 1 03-FEB-00 1DB6 0
JRNL AUTH S.A.ROBERTSON,K.HARADA,A.D.FRANKEL,D.E.WEMMER
JRNL TITL STRUCTURE DETERMINATION AND BINDING KINETICS OF A DNA
JRNL TITL 2 APTAMER-ARGININAMIDE COMPLEX.
JRNL REF BIOCHEMISTRY V. 39 946 2000
JRNL REFN ISSN 0006-2960
JRNL PMID 10653638
JRNL DOI 10.1021/BI9915061
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH K.HARADA,A.D.FRANKEL
REMARK 1 TITL IDENTIFICATION OF TWO NOVEL ARGININE BINDING DNAS
REMARK 1 REF EMBO J. V. 14 5798 1995
REMARK 1 REFN ISSN 0261-4189
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : FELIX 950, DISCOVER 2.97
REMARK 3 AUTHORS : MOLECULAR SIMULATIONS, INC (FELIX), MOLECULAR
REMARK 3 SIMULATIONS, INC (DISCOVER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1DB6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-NOV-99.
REMARK 100 THE DEPOSITION ID IS D_1000009942.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 293; 278
REMARK 210 PH : 6.2; 6.2
REMARK 210 IONIC STRENGTH : 0-25 MM NACL; 0-25 MM NACL
REMARK 210 PRESSURE : AMBIENT; AMBIENT
REMARK 210 SAMPLE CONTENTS : 1.44 MM DNA, 10 MM SODIUM
REMARK 210 PHOSPHATE BUFFER, PH 6.2, 0.05
REMARK 210 MM EDTA, 0-25 MM NACL, 8-10
REMARK 210 EQUIVALENTS ARGININAMIDE; 1.44
REMARK 210 MM DNA, 10 MM SODIUM PHOSPHATE
REMARK 210 BUFFER, PH 6.2, 0.05 MM EDTA, 0-
REMARK 210 25 MM NACL, 8-10 EQUIVALENTS
REMARK 210 ARGININAMIDE
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; TOCSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : OMEGA; AMX
REMARK 210 SPECTROMETER MANUFACTURER : GE; BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : MARDIGRAS 3.2
REMARK 210 METHOD USED : DISTANCE RESTRAINTS WERE
REMARK 210 OBTAINED FROM RELAXATION RATE
REMARK 210 MATRIX CALCULATIONS. STRUCTURES
REMARK 210 WERE CALCULATED USING SIMULATED
REMARK 210 ANNEALING AND MOLECULAR DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 30
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE
REMARK 210 COVALENT GEOMETRY,STRUCTURES
REMARK 210 WITH FAVORABLE NON- BOND ENERGY,
REMARK 210 STRUCTURES WITH THE LEAST
REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES
REMARK 210 WITH THE LOWEST ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 6
REMARK 210
REMARK 210 REMARK: DATA WERE ALSO COLLECTED FOR SEQUENCES CONTAINING 5-METHYL
REMARK 210 CYTOSINE SUBSTITUTED INDEPENDENTLY AT POSITIONS 15 AND 16, AND
REMARK 210 FOR THE SEQUENCE WITH INOSINE SUBSTITUTED AT POSTION 14.
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: 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 H3 DT A 10 O6 DG A 14 1.57
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 2 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES
REMARK 500 1 DC A 4 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 1 DA A 7 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES
REMARK 500 1 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES
REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 1 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES
REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES
REMARK 500 1 DC A 16 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 1 DT A 17 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 1 DG A 18 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 1 DG A 19 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 1 DT A 20 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES
REMARK 500 1 DC A 21 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 1 DG A 22 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 2 DC A 4 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 2 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES
REMARK 500 2 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 2 DA A 7 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES
REMARK 500 2 DC A 8 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 2 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 2 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES
REMARK 500 2 DG A 11 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 2 DC A 13 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 2 DC A 16 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 2 DG A 18 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES
REMARK 500 2 DC A 21 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 2 DG A 22 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 3 DG A 2 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES
REMARK 500 3 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES
REMARK 500 3 DC A 4 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 3 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 3 DA A 7 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 3 DC A 8 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 3 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 3 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 3 DT A 12 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES
REMARK 500 3 DT A 12 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES
REMARK 500 3 DC A 13 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 3 DC A 16 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 3 DG A 18 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 3 DG A 19 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES
REMARK 500 3 DC A 21 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 3 DG A 22 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 4 DG A 2 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 4 DC A 4 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 4 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES
REMARK 500 4 DA A 6 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 4 DA A 7 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 152 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 DC A 15 0.07 SIDE CHAIN
REMARK 500 1 DC A 16 0.11 SIDE CHAIN
REMARK 500 2 DC A 1 0.07 SIDE CHAIN
REMARK 500 2 DG A 14 0.07 SIDE CHAIN
REMARK 500 2 DC A 15 0.08 SIDE CHAIN
REMARK 500 2 DC A 16 0.06 SIDE CHAIN
REMARK 500 3 DC A 1 0.07 SIDE CHAIN
REMARK 500 3 DT A 10 0.07 SIDE CHAIN
REMARK 500 3 DG A 14 0.08 SIDE CHAIN
REMARK 500 3 DC A 15 0.09 SIDE CHAIN
REMARK 500 3 DC A 16 0.07 SIDE CHAIN
REMARK 500 4 DC A 1 0.07 SIDE CHAIN
REMARK 500 4 DG A 14 0.08 SIDE CHAIN
REMARK 500 4 DC A 15 0.06 SIDE CHAIN
REMARK 500 4 DC A 16 0.06 SIDE CHAIN
REMARK 500 5 DC A 8 0.06 SIDE CHAIN
REMARK 500 5 DT A 12 0.07 SIDE CHAIN
REMARK 500 5 DG A 14 0.08 SIDE CHAIN
REMARK 500 5 DC A 15 0.08 SIDE CHAIN
REMARK 500 5 DC A 16 0.08 SIDE CHAIN
REMARK 500 6 DC A 1 0.06 SIDE CHAIN
REMARK 500 6 DG A 14 0.08 SIDE CHAIN
REMARK 500 6 DC A 15 0.06 SIDE CHAIN
REMARK 500 7 DC A 1 0.07 SIDE CHAIN
REMARK 500 7 DG A 14 0.07 SIDE CHAIN
REMARK 500 7 DC A 15 0.10 SIDE CHAIN
REMARK 500 7 DC A 16 0.09 SIDE CHAIN
REMARK 500 8 DC A 1 0.07 SIDE CHAIN
REMARK 500 8 DG A 14 0.09 SIDE CHAIN
REMARK 500 8 DC A 15 0.11 SIDE CHAIN
REMARK 500 8 DC A 16 0.10 SIDE CHAIN
REMARK 500 9 DC A 1 0.07 SIDE CHAIN
REMARK 500 9 DG A 14 0.06 SIDE CHAIN
REMARK 500 9 DC A 15 0.09 SIDE CHAIN
REMARK 500 9 DC A 16 0.09 SIDE CHAIN
REMARK 500 10 DC A 1 0.06 SIDE CHAIN
REMARK 500 10 DG A 14 0.09 SIDE CHAIN
REMARK 500 10 DC A 15 0.08 SIDE CHAIN
REMARK 500 10 DC A 16 0.09 SIDE CHAIN
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 AAR A 23
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2ARG RELATED DB: PDB
REMARK 900 2ARG CONTAINS A DIFFERENT DNA APTAMER COMPLEXED WITH ARGININAMIDE
REMARK 900 RELATED ID: 1OLD RELATED DB: PDB
REMARK 900 1OLD IS A SIMILAR DNA APTAMER
DBREF 1DB6 A 1 22 PDB 1DB6 1DB6 1 22
SEQRES 1 A 22 DC DG DA DC DC DA DA DC DG DT DG DT DC
SEQRES 2 A 22 DG DC DC DT DG DG DT DC DG
HET AAR A 23 28
HETNAM AAR ARGININEAMIDE
FORMUL 2 AAR C6 H16 N5 O 1+
SITE 1 AC1 8 DC A 8 DG A 9 DT A 12 DC A 13
SITE 2 AC1 8 DG A 14 DC A 16 DT A 17 DG A 18
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