HEADER DNA 03-DEC-05 2F8U TITLE G-QUADRUPLEX STRUCTURE FORMED IN HUMAN BCL-2 PROMOTER, HYBRID FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*GP*GP*CP*GP*CP*GP*GP*GP*AP*GP*GP*AP*AP*TP*TP*GP*GP COMPND 3 *GP*CP*GP*GP*G)-3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: G-QUADRUPLEX OF BCL-2 PROMOTER SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS G-QUADRUPLEX, BCL-2 PROMOTER, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.DAI,D.CHEN,M.CARVER,D.YANG REVDAT 4 17-SEP-14 2F8U 1 REMARK TITLE VERSN REVDAT 3 24-FEB-09 2F8U 1 VERSN REVDAT 2 21-NOV-06 2F8U 1 JRNL REVDAT 1 07-NOV-06 2F8U 0 JRNL AUTH J.DAI,D.CHEN,R.A.JONES,L.H.HURLEY,D.YANG JRNL TITL NMR SOLUTION STRUCTURE OF THE MAJOR G-QUADRUPLEX STRUCTURE JRNL TITL 2 FORMED IN THE HUMAN BCL2 PROMOTER REGION. JRNL REF NUCLEIC ACIDS RES. V. 34 5133 2006 JRNL REFN ISSN 0305-1048 JRNL PMID 16998187 JRNL DOI 10.1093/NAR/GKL610 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER, A.T. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2F8U COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-DEC-05. REMARK 100 THE RCSB ID CODE IS RCSB035595. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 308; 288; 280; 274 REMARK 210 PH : 7.0; 7.0; 7.0; 7.0; 7.0 REMARK 210 IONIC STRENGTH : 60MM; 60MM; 60MM; 60MM; 60MM REMARK 210 PRESSURE : 1ATM; 1ATM; 1ATM; 1ATM; 1ATM REMARK 210 SAMPLE CONTENTS : 1MM DNA OLIGOMER, 20MM POTASSIUM REMARK 210 PHOSPHATE BUFFER, 40MM POTASSIUM REMARK 210 CHLORIDE, 90% H2O, 10% D2O; 1MM REMARK 210 DNA OLIGOMER, 20MM POTASSIUM REMARK 210 PHOSPHATE BUFFER, 40MM POTASSIUM REMARK 210 CHLORIDE, 99.99% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY; PE REMARK 210 -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 : XWINNMR 3.5, SPARKY 3.110 REMARK 210 METHOD USED : DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : 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 : 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 9 DT A 16 C5 DT A 16 C7 0.037 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 1 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 1 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DG A 3 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DC A 4 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 5 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 5 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DC 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 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 7 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 8 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG A 9 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 9 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DA A 10 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DA A 10 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 11 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 11 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 12 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DG A 12 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DA A 13 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DA A 13 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA A 14 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DA A 14 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DT A 15 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DT A 16 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 17 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 17 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 17 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 DG A 18 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG A 18 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 18 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DG A 19 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG A 19 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 19 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DC A 20 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DG A 21 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 21 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 21 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DG A 22 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 558 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 8 DT A 15 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XAV RELATED DB: PDB REMARK 900 RELATED ID: 2LBY RELATED DB: PDB REMARK 900 RELATED ID: 2M27 RELATED DB: PDB DBREF 2F8U A 1 23 PDB 2F8U 2F8U 1 23 SEQRES 1 A 23 DG DG DG DC DG DC DG DG DG DA DG DG DA SEQRES 2 A 23 DA DT DT DG DG DG DC 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