HEADER DNA 01-DEC-06 2O3M TITLE MONOMERIC G-DNA TETRAPLEX FROM HUMAN C-KIT PROMOTER COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*CP*TP*GP*GP*GP*AP*GP*GP COMPND 3 *AP*GP*GP*G)-3'; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: C-KIT PROMOTER FRAGMENT SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS G-TETRAD;PARALLEL G-QUADRUPLEX; EDGEWISE, SINGLE-RESIDUE CHA KEYWDS 2 REVERSAL, 5-NUCLEOTIDE SNAP-BACK LOOPS;BROKEN STRAND TOPOLOG, DNA EXPDTA SOLUTION NMR NUMMDL 11 AUTHOR A.T.PHAN,V.V.KURYAVYI,S.BURGE,S.NEIDLE,D.J.PATEL REVDAT 4 27-DEC-23 2O3M 1 REMARK REVDAT 3 16-MAR-22 2O3M 1 REMARK REVDAT 2 24-FEB-09 2O3M 1 VERSN REVDAT 1 22-MAY-07 2O3M 0 JRNL AUTH A.T.PHAN,V.V.KURYAVYI,S.BURGE,S.NEIDLE,D.J.PATEL JRNL TITL STRUCTURE OF AN UNPRECEDENTED G-QUADRUPLEX SCAFFOLD IN THE JRNL TITL 2 HUMAN C-KIT PROMOTER. JRNL REF J.AM.CHEM.SOC. V. 129 4386 2007 JRNL REFN ISSN 0002-7863 JRNL PMID 17362008 JRNL DOI 10.1021/JA068739H REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : AT BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2O3M COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-DEC-06. REMARK 100 THE DEPOSITION ID IS D_1000040644. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 70 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 70 MM KCL 20 MM POTASSIUM REMARK 210 PHOSPHATE, 90% H2O 10% D2O; 70 REMARK 210 MM KCL 20 MM POTASSIUM PHOSPHATE, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1H-1H NOESY; 1H-1H TOCSY; 1H- REMARK 210 31P COSY; 1H-1H COSY; 1H-15N REMARK 210 JRHMQC; 1H-15N HMBC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.0, FELIX 2000 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS CARTESIAN REMARK 210 DYNAMICS MATRIX RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM 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 12 C5 DT A 12 C7 0.036 REMARK 500 2 DT A 12 C5 DT A 12 C7 0.036 REMARK 500 3 DT A 12 C5 DT A 12 C7 0.037 REMARK 500 5 DT A 12 C5 DT A 12 C7 0.036 REMARK 500 6 DT A 12 C5 DT A 12 C7 0.037 REMARK 500 7 DT A 12 C5 DT A 12 C7 0.039 REMARK 500 8 DT A 12 C5 DT A 12 C7 0.037 REMARK 500 10 DT A 12 C5 DT A 12 C7 0.036 REMARK 500 11 DT A 12 C5 DT A 12 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 DA A 1 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DA A 5 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DC A 9 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DT A 12 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DG A 14 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 15 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 16 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 17 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG A 18 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA A 19 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DG A 20 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 21 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DG A 22 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DA A 1 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DC A 9 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DG A 10 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DT A 12 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DG A 14 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DG A 15 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DA A 16 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DG A 17 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DG A 18 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DA A 19 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DG A 20 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DG A 21 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 DA A 1 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 3 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 3 DG A 7 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 238 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2A5P RELATED DB: PDB REMARK 900 G-QUADRUPLEX IN HUMAN C-MYC PROMOTER DBREF 2O3M A 1 22 PDB 2O3M 2O3M 1 22 SEQRES 1 A 22 DA DG DG DG DA DG DG DG DC DG DC DT DG SEQRES 2 A 22 DG DG DA DG DG DA DG 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