HEADER DNA 05-JUL-18 6A7Y TITLE SOLUTION STRUCTURE OF AN INTERMOLECULAR LEAPED V-SHAPE G-QUADRUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*GP*GP*TP*TP*TP*TP*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*TP*GP*GP*GP*GP*A)-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STERKIELLA NOVA; SOURCE 3 ORGANISM_TAXID: 200597; SOURCE 4 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 32630; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: STERKIELLA NOVA; SOURCE 8 ORGANISM_TAXID: 200597; SOURCE 9 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS G-QUADRUPLEX, V-SHAPE, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR C.J.WAN,N.ZHANG REVDAT 4 15-MAY-24 6A7Y 1 REMARK REVDAT 3 14-JUN-23 6A7Y 1 REMARK REVDAT 2 10-JUL-19 6A7Y 1 JRNL REMARK REVDAT 1 12-DEC-18 6A7Y 0 JRNL AUTH C.WAN,W.FU,H.JING,N.ZHANG JRNL TITL NMR SOLUTION STRUCTURE OF AN ASYMMETRIC INTERMOLECULAR JRNL TITL 2 LEAPED V-SHAPE G-QUADRUPLEX: SELECTIVE RECOGNITION OF THE JRNL TITL 3 D(G2NG3NG4) SEQUENCE MOTIF BY A SHORT LINEAR G-RICH DNA JRNL TITL 4 PROBE. JRNL REF NUCLEIC ACIDS RES. V. 47 1544 2019 JRNL REFN ESSN 1362-4962 JRNL PMID 30445650 JRNL DOI 10.1093/NAR/GKY1167 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 6A7Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1300008299. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2 MM DNA (5' REMARK 210 -D(*GP*GP*TP*TP*TP*TP*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'), 2 REMARK 210 MM DNA (5'-D(*TP*GP*GP*GP*GP*A)-3'), 90% H2O/10% D2O; 2 MM DNA REMARK 210 (5'-D(*GP*GP*TP*TP*TP*TP*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'), REMARK 210 2 MM DNA (5'-D(*TP*GP*GP*GP*GP*A)-3'), 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-15N HSQC; REMARK 210 2D 1H-13C HSQC; 2D DQF-COSY; 2D REMARK 210 1H-13C HMBC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, X-PLOR NIH, ANALYSIS, REMARK 210 TOPSPIN, NMRPIPE REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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 : 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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. = 2.2 DEGREES REMARK 500 1 DT A 3 N3 - C2 - O2 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DT A 3 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DT A 5 N3 - C2 - O2 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DT A 6 N3 - C2 - O2 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT A 11 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT A 11 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT A 11 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DT A 12 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DT A 13 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DT A 13 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DT A 14 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT A 14 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DG A 15 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 15 N3 - C4 - C5 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DG A 16 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG A 16 N3 - C4 - C5 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DG A 16 N3 - C4 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DT B 19 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DG B 20 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DG B 21 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG B 23 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DA B 24 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA B 24 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA B 24 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DT A 3 N3 - C2 - O2 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DT A 3 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 DT A 4 N3 - C2 - O2 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 2 DT A 5 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 2 DT A 6 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DT A 6 N3 - C2 - O2 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DG A 10 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DT A 11 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT A 11 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DT A 12 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 DT A 13 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DT A 13 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT A 13 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 330 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36199 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF AN INTERMOLECULAR LEAPED V-SHAPE G-QUADRUPLEX REMARK 999 REMARK 999 SEQUENCE REMARK 999 CHAIN B HAS A T-TO-A MUTATED SEQUENCE. THE ORIGINAL SEQUENCE IS REMARK 999 D(TGGGGT). DBREF 6A7Y A 1 18 PDB 6A7Y 6A7Y 1 18 DBREF 6A7Y B 19 24 PDB 6A7Y 6A7Y 19 24 SEQRES 1 A 18 DG DG DT DT DT DT DG DG DG DG DT DT DT SEQRES 2 A 18 DT DG DG DG DG SEQRES 1 B 6 DT DG DG DG DG DA 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