HEADER DNA 11-OCT-24 9JX5 TITLE SOLUTION NMR STRUCTURE OF THE 1:1 COMPLEX OF NOP56 INTRONIC G- TITLE 2 QUADRUPLEX BOUND WITH PYRIDOSTATIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*G)- COMPND 4 3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS ANTIPARALLEL G4, NOP56 ONCOGENE, PDS, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR Z.YAN,L.WAN,P.GUO,D.HAN REVDAT 1 05-FEB-25 9JX5 0 JRNL AUTH Z.YAN,L.WAN,P.GUO,D.HAN JRNL TITL STRUCTURAL INSIGHTS INTO AN ANTIPARALLEL CHAIR-TYPE JRNL TITL 2 G-QUADRUPLEX FROM THE INTRON OF NOP56 ONCOGENE JRNL REF TO BE PUBLISHED JRNL REFN 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 9JX5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1300052496. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 1 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM DNA (5' REMARK 210 -D(*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP* REMARK 210 G)-3'), 1 MM SODIUM PHOSPHATE, 0.02 MM DSS, 1.5 MM PYRIDOSTATIN, REMARK 210 99.96% D2O; 0.5 MM DNA (5'-D(*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP* REMARK 210 TP*GP*GP*GP*CP*CP*TP*GP*GP*G)-3'), 1 MM SODIUM PHOSPHATE, 0.02 REMARK 210 MM DSS, 1.5 MM PYRIDOSTATIN, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-1H COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 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: 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 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. = 2.8 DEGREES REMARK 500 1 DG A 2 N3 - C4 - C5 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 7.0 DEGREES REMARK 500 1 DC A 4 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DG A 7 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DC A 10 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DC A 11 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 7.3 DEGREES REMARK 500 1 DG A 13 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DG A 14 O4' - C1' - C2' ANGL. DEV. = -6.0 DEGREES REMARK 500 1 DG A 14 O4' - C1' - N9 ANGL. DEV. = 6.9 DEGREES REMARK 500 1 DG A 14 N3 - C4 - C5 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DG A 14 N3 - C4 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DG A 15 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DC A 16 O4' - C1' - N1 ANGL. DEV. = 8.1 DEGREES REMARK 500 1 DC A 17 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 19 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DG A 19 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 1 DG A 20 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG A 21 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 2 DG A 1 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DG A 3 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 2 DC A 4 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DC A 5 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DG A 7 C3' - O3' - P ANGL. DEV. = 9.5 DEGREES REMARK 500 2 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DC A 11 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DC A 11 C3' - O3' - P ANGL. DEV. = 7.9 DEGREES REMARK 500 2 DT A 12 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DG A 13 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 DG A 14 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 2 DG A 14 O4' - C1' - C2' ANGL. DEV. = -5.7 DEGREES REMARK 500 2 DG A 14 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 2 DG A 14 N3 - C4 - C5 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 DG A 15 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DC A 16 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 2 DC A 17 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 DT A 18 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DG A 19 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DG A 19 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 2 DG A 20 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DG A 21 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 255 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 DG A 2 0.07 SIDE CHAIN REMARK 500 1 DG A 3 0.09 SIDE CHAIN REMARK 500 1 DC A 10 0.07 SIDE CHAIN REMARK 500 1 DC A 11 0.08 SIDE CHAIN REMARK 500 1 DT A 12 0.07 SIDE CHAIN REMARK 500 1 DG A 13 0.11 SIDE CHAIN REMARK 500 1 DC A 16 0.06 SIDE CHAIN REMARK 500 1 DC A 17 0.12 SIDE CHAIN REMARK 500 1 DG A 21 0.10 SIDE CHAIN REMARK 500 2 DG A 2 0.07 SIDE CHAIN REMARK 500 2 DG A 3 0.08 SIDE CHAIN REMARK 500 2 DC A 5 0.08 SIDE CHAIN REMARK 500 2 DG A 13 0.07 SIDE CHAIN REMARK 500 2 DG A 15 0.06 SIDE CHAIN REMARK 500 2 DG A 21 0.10 SIDE CHAIN REMARK 500 3 DG A 2 0.07 SIDE CHAIN REMARK 500 3 DG A 3 0.09 SIDE CHAIN REMARK 500 3 DG A 13 0.08 SIDE CHAIN REMARK 500 3 DC A 16 0.07 SIDE CHAIN REMARK 500 3 DC A 17 0.07 SIDE CHAIN REMARK 500 3 DG A 21 0.14 SIDE CHAIN REMARK 500 4 DG A 1 0.07 SIDE CHAIN REMARK 500 4 DG A 2 0.05 SIDE CHAIN REMARK 500 4 DG A 3 0.07 SIDE CHAIN REMARK 500 4 DG A 7 0.06 SIDE CHAIN REMARK 500 4 DT A 12 0.09 SIDE CHAIN REMARK 500 4 DG A 13 0.09 SIDE CHAIN REMARK 500 4 DG A 15 0.07 SIDE CHAIN REMARK 500 4 DT A 18 0.09 SIDE CHAIN REMARK 500 4 DG A 21 0.14 SIDE CHAIN REMARK 500 5 DG A 1 0.06 SIDE CHAIN REMARK 500 5 DG A 2 0.07 SIDE CHAIN REMARK 500 5 DG A 3 0.08 SIDE CHAIN REMARK 500 5 DG A 13 0.08 SIDE CHAIN REMARK 500 5 DG A 21 0.11 SIDE CHAIN REMARK 500 6 DG A 1 0.06 SIDE CHAIN REMARK 500 6 DG A 2 0.10 SIDE CHAIN REMARK 500 6 DG A 3 0.06 SIDE CHAIN REMARK 500 6 DC A 5 0.09 SIDE CHAIN REMARK 500 6 DT A 6 0.09 SIDE CHAIN REMARK 500 6 DG A 13 0.08 SIDE CHAIN REMARK 500 6 DG A 21 0.09 SIDE CHAIN REMARK 500 7 DG A 1 0.07 SIDE CHAIN REMARK 500 7 DG A 2 0.07 SIDE CHAIN REMARK 500 7 DG A 3 0.08 SIDE CHAIN REMARK 500 7 DG A 7 0.06 SIDE CHAIN REMARK 500 7 DG A 13 0.10 SIDE CHAIN REMARK 500 7 DG A 21 0.12 SIDE CHAIN REMARK 500 8 DG A 1 0.05 SIDE CHAIN REMARK 500 8 DG A 2 0.07 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 61 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 N36+H33+H34+H35, N40+H30+H31+H32 AND N52+H95+H96+H97 ARE THREE REMARK 600 PROTONATED (POSITIVE CHARGED) AMINO GROUPS. THEREFORE THE VALENCE REMARK 600 OF N36, N40 AND N52 IS FOUR. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36698 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF THE 1:1 COMPLEX OF NOP56 INTRONIC G- REMARK 900 QUADRUPLEX BOUND WITH PYRIDOSTATIN DBREF 9JX5 A 1 21 PDB 9JX5 9JX5 1 21 SEQRES 1 A 21 DG DG DG DC DC DT DG DG DG DC DC DT DG SEQRES 2 A 21 DG DG DC DC DT DG DG DG HET 7V8 A 101 79 HETNAM 7V8 4-(2-AZANYLETHOXY)-N2,N6-BIS[4-(2-AZANYLETHOXY) HETNAM 2 7V8 QUINOLIN-2-YL]PYRIDINE-2,6-DICARBOXAMIDE HETSYN 7V8 PYRIDOSTATIN FORMUL 2 7V8 C31 H32 N8 O5 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