HEADER DNA 21-JUL-23 8PWR
TITLE TINA-CONJUGATED ANTIPARALLEL DNA TRIPLEX
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*TP*CP*CP*TP*CP*CP*T)-3');
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: DNA (5'-D(*AP*GP*GP*AP*GP*GP*A)-3');
COMPND 7 CHAIN: B;
COMPND 8 ENGINEERED: YES;
COMPND 9 MOL_ID: 3;
COMPND 10 MOLECULE: DNA (5'-D(*TP*GP*GP*TP*GP*(J32)P*GP*T)-3');
COMPND 11 CHAIN: C;
COMPND 12 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 MOL_ID: 2;
SOURCE 6 SYNTHETIC: YES;
SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 8 ORGANISM_TAXID: 9606;
SOURCE 9 MOL_ID: 3;
SOURCE 10 SYNTHETIC: YES;
SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 12 ORGANISM_TAXID: 9606
KEYWDS TRIPLEX, TINA, ANTIPARALLEL, CONJUGATE, DNA
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR M.GARAVIS,P.J.B.EDWARDS,I.SERRANO-CHACON,O.DOLUCA,V.V.FILICHEV,
AUTHOR 2 C.GONZALEZ
REVDAT 3 27-MAR-24 8PWR 1 JRNL
REVDAT 2 07-FEB-24 8PWR 1 JRNL
REVDAT 1 17-JAN-24 8PWR 0
SPRSDE 17-JAN-24 8PWR 6QHI
JRNL AUTH M.GARAVIS,P.J.B.EDWARDS,I.SERRANO-CHACON,O.DOLUCA,
JRNL AUTH 2 V.V.FILICHEV,C.GONZALEZ
JRNL TITL UNDERSTANDING INTERCALATIVE MODULATION OF G-RICH SEQUENCE
JRNL TITL 2 FOLDING: SOLUTION STRUCTURE OF A TINA-CONJUGATED
JRNL TITL 3 ANTIPARALLEL DNA TRIPLEX.
JRNL REF NUCLEIC ACIDS RES. V. 52 2686 2024
JRNL REFN ESSN 1362-4962
JRNL PMID 38281138
JRNL DOI 10.1093/NAR/GKAE028
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : AMBER
REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG,
REMARK 3 DUKE, LUO, ... AND KOLLMAN
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 8PWR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-JUL-23.
REMARK 100 THE DEPOSITION ID IS D_1292132112.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 279.6; 300.4
REMARK 210 PH : 7; 7
REMARK 210 IONIC STRENGTH : 125; 125
REMARK 210 PRESSURE : 1 ATM; 1 ATM
REMARK 210 SAMPLE CONTENTS : 0.5 MM TRIPLEX-TINA, 90% H2O/10%
REMARK 210 D2O; 0.5 MM TRIPLEX-TINA, 90%
REMARK 210 H2O/10% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY;
REMARK 210 2D DQF-COSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NMRFAM-SPARKY, TOPSPIN
REMARK 210 METHOD USED : MOLECULAR DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 15
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST
REMARK 210 ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 2
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: TRIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C
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 DA B 8 C5' DA B 8 C4' 0.044
REMARK 500 3 DT A 7 C5 DT A 7 C7 0.036
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 DT A 1 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES
REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -5.1 DEGREES
REMARK 500 1 DC A 6 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 1 DG B 9 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 1 DG B 10 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DA B 14 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DT C 15 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES
REMARK 500 1 DG C 16 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 1 DG C 19 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 1 X0K C 20 C3' - O3' - P ANGL. DEV. = 44.9 DEGREES
REMARK 500 1 DG C 21 O4' - C1' - C2' ANGL. DEV. = -6.2 DEGREES
REMARK 500 1 DT C 22 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES
REMARK 500 2 DT A 1 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES
REMARK 500 2 DT A 1 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES
REMARK 500 2 DC A 2 O3' - P - O5' ANGL. DEV. = 41.9 DEGREES
REMARK 500 2 DC A 2 O3' - P - OP2 ANGL. DEV. = -20.7 DEGREES
REMARK 500 2 DC A 2 O3' - P - OP1 ANGL. DEV. = -22.4 DEGREES
REMARK 500 2 DC A 2 OP1 - P - OP2 ANGL. DEV. = 11.9 DEGREES
REMARK 500 2 DC A 2 O5' - P - OP1 ANGL. DEV. = -22.6 DEGREES
REMARK 500 2 DC A 2 O5' - P - OP2 ANGL. DEV. = -23.7 DEGREES
REMARK 500 2 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.8 DEGREES
REMARK 500 2 DC A 6 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 2 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 2 DT A 7 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES
REMARK 500 2 DG B 9 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 2 DG B 10 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES
REMARK 500 2 DG B 13 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 2 DA B 14 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES
REMARK 500 2 DG C 16 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 2 DG C 19 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES
REMARK 500 2 X0K C 20 C3' - O3' - P ANGL. DEV. = 44.2 DEGREES
REMARK 500 2 DG C 21 O4' - C1' - C2' ANGL. DEV. = -6.5 DEGREES
REMARK 500 2 DT C 22 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 3 DC A 2 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 3 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES
REMARK 500 3 DC A 5 N3 - C4 - N4 ANGL. DEV. = -4.8 DEGREES
REMARK 500 3 DC A 6 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 3 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 3 DG B 9 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 3 DG B 10 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES
REMARK 500 3 DA B 11 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES
REMARK 500 3 DA B 11 N1 - C6 - N6 ANGL. DEV. = -3.7 DEGREES
REMARK 500 3 DA B 14 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 3 DG C 16 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES
REMARK 500 3 DG C 16 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 3 DG C 16 N1 - C6 - O6 ANGL. DEV. = -7.0 DEGREES
REMARK 500 3 DG C 19 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 3 X0K C 20 C3' - O3' - P ANGL. DEV. = 45.3 DEGREES
REMARK 500 3 DG C 21 O4' - C1' - C2' ANGL. DEV. = -6.2 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 137 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 DT A 7 0.11 SIDE CHAIN
REMARK 500 1 DA B 11 0.05 SIDE CHAIN
REMARK 500 1 DT C 15 0.07 SIDE CHAIN
REMARK 500 2 DC A 3 0.06 SIDE CHAIN
REMARK 500 2 DT A 7 0.10 SIDE CHAIN
REMARK 500 2 DG B 9 0.11 SIDE CHAIN
REMARK 500 2 DA B 11 0.06 SIDE CHAIN
REMARK 500 2 DT C 15 0.09 SIDE CHAIN
REMARK 500 2 DG C 16 0.06 SIDE CHAIN
REMARK 500 2 DT C 18 0.07 SIDE CHAIN
REMARK 500 3 DT A 1 0.07 SIDE CHAIN
REMARK 500 3 DC A 3 0.08 SIDE CHAIN
REMARK 500 3 DT A 7 0.09 SIDE CHAIN
REMARK 500 3 DG B 9 0.09 SIDE CHAIN
REMARK 500 3 DT C 15 0.08 SIDE CHAIN
REMARK 500 3 DT C 18 0.10 SIDE CHAIN
REMARK 500 4 DT A 7 0.08 SIDE CHAIN
REMARK 500 4 DG B 9 0.09 SIDE CHAIN
REMARK 500 4 DT C 15 0.10 SIDE CHAIN
REMARK 500 4 DG C 16 0.06 SIDE CHAIN
REMARK 500 4 DT C 18 0.09 SIDE CHAIN
REMARK 500 5 DT A 1 0.09 SIDE CHAIN
REMARK 500 5 DT A 7 0.10 SIDE CHAIN
REMARK 500 5 DG B 9 0.10 SIDE CHAIN
REMARK 500 5 DT C 15 0.10 SIDE CHAIN
REMARK 500 5 DT C 18 0.11 SIDE CHAIN
REMARK 500 6 DT A 7 0.10 SIDE CHAIN
REMARK 500 6 DG B 9 0.06 SIDE CHAIN
REMARK 500 6 DT C 15 0.09 SIDE CHAIN
REMARK 500 6 DT C 18 0.10 SIDE CHAIN
REMARK 500 7 DT A 7 0.08 SIDE CHAIN
REMARK 500 7 DG B 9 0.07 SIDE CHAIN
REMARK 500 7 DT C 15 0.07 SIDE CHAIN
REMARK 500 7 DT C 18 0.11 SIDE CHAIN
REMARK 500 8 DT A 7 0.09 SIDE CHAIN
REMARK 500 8 DG B 9 0.06 SIDE CHAIN
REMARK 500 8 DT C 15 0.09 SIDE CHAIN
REMARK 500 8 DT C 18 0.07 SIDE CHAIN
REMARK 500 8 DG C 21 0.06 SIDE CHAIN
REMARK 500 8 DT C 22 0.07 SIDE CHAIN
REMARK 500 9 DT A 7 0.10 SIDE CHAIN
REMARK 500 9 DG B 9 0.07 SIDE CHAIN
REMARK 500 9 DT C 15 0.09 SIDE CHAIN
REMARK 500 9 DT C 18 0.07 SIDE CHAIN
REMARK 500 10 DT A 1 0.06 SIDE CHAIN
REMARK 500 10 DC A 3 0.06 SIDE CHAIN
REMARK 500 10 DT A 7 0.09 SIDE CHAIN
REMARK 500 10 DG B 9 0.06 SIDE CHAIN
REMARK 500 10 DT C 15 0.09 SIDE CHAIN
REMARK 500 10 DT C 18 0.09 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 34836 RELATED DB: BMRB
REMARK 900 TINA-CONJUGATED ANTIPARALLEL DNA TRIPLEX
DBREF 8PWR A 1 7 PDB 8PWR 8PWR 1 7
DBREF 8PWR B 8 14 PDB 8PWR 8PWR 8 14
DBREF 8PWR C 15 22 PDB 8PWR 8PWR 15 22
SEQRES 1 A 7 DT DC DC DT DC DC DT
SEQRES 1 B 7 DA DG DG DA DG DG DA
SEQRES 1 C 8 DT DG DG DT DG X0K DG DT
HET X0K C 20 54
HETNAM X0K [(2~{S})-2-OXIDANYL-3-[[4-(2-PYREN-1-YLETHYNYL)
HETNAM 2 X0K PHENYL]METHOXY]PROPYL] DIHYDROGEN PHOSPHITE
FORMUL 3 X0K C28 H23 O5 P
LINK O3' DG C 19 P X0K C 20 1555 1555 1.62
LINK O3' X0K C 20 P DG C 21 1555 1555 1.61
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