HEADER DNA 27-JUN-01 1JHI TITLE SOLUTION STRUCTURE OF A HEDAMYCIN-DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*CP*CP*(HEH)GP*GP*T)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: HEDAMYCIN-DNA SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DUPLEX DNA, HEDAMYCIN, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR E.A.OWEN,G.A.BURLEY,J.A.CARVER,G.WICKHAM,M.A.KENIRY REVDAT 3 23-FEB-22 1JHI 1 REMARK LINK REVDAT 2 24-FEB-09 1JHI 1 VERSN REVDAT 1 08-JUL-03 1JHI 0 JRNL AUTH E.A.OWEN,G.A.BURLEY,J.A.CARVER,G.WICKHAM,M.A.KENIRY JRNL TITL STRUCTURAL INVESTIGATION OF THE HEDAMYCIN:D(ACCGGT)2 COMPLEX JRNL TITL 2 BY NMR AND RESTRAINED MOLECULAR DYNAMICS. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 290 1602 2002 JRNL REFN ISSN 0006-291X JRNL PMID 11820806 JRNL DOI 10.1006/BBRC.2002.6369 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : MARDIGRAS 3.2, CHARMM 23.2, CNS_SOLVE 1.0, CORMA REMARK 3 5.2 REMARK 3 AUTHORS : BORGAIS, B. AND JAMES, T.L. (MARDIGRAS), MOLECULAR REMARK 3 SIMULATIONS INCORPORATED, WALTHAM MA (CHARMM), REMARK 3 BRUNGER,A.T., ADAMS,P.D., CLORE,G.M., DELANO,W.L., REMARK 3 GROS,P. GROSSE-KUNSTLEVE,R.W., JIANG,T-S., REMARK 3 KUSZEWSKI,J., NILGES,M., PANNU,N.S., READ,R.J., REMARK 3 RICE,L.M., SIMONSON,T., WARREN,G.L. (CNS_SOLVE), REMARK 3 KEEPERS,J. AND JAMES, T. L. (CORMA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1JHI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUN-01. REMARK 100 THE DEPOSITION ID IS D_1000013777. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 6.7 REMARK 210 IONIC STRENGTH : 0.05 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : HEDAMYCIN COVALENTLY BOUND TO G4 REMARK 210 OF D(ACCGGT); HEDAMYCIN REMARK 210 COVALENTLY BOUND TO G4 OF REMARK 210 D(ACCGGT) REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.1, XEASY 1.3.10 REMARK 210 METHOD USED : FULL RELAXATION MATRIX REMARK 210 REFINEMENT RESTRAINED MOLECULAR REMARK 210 DYNAMICS TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : THE 10 STRUCTURES SUBMITTED ARE REMARK 210 THOSE WITH THE LOWEST ENERGY,AND REMARK 210 AGREE BEST WITH THE NMR DATA. REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 7 REMARK 210 REMARK 210 REMARK: THE DATA WAS COLLECTED AND PROCESSED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES 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 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 DC A 2 C5 DC A 2 C6 0.051 REMARK 500 1 DC A 3 N1 DC A 3 C6 -0.037 REMARK 500 1 DG A 4 N7 DG A 4 C8 0.040 REMARK 500 1 DG A 5 N7 DG A 5 C8 0.042 REMARK 500 1 DT A 6 C5 DT A 6 C6 0.045 REMARK 500 1 DT A 6 C6 DT A 6 N1 -0.045 REMARK 500 1 DC B 8 C5 DC B 8 C6 0.048 REMARK 500 1 DC B 9 N1 DC B 9 C6 -0.037 REMARK 500 1 DG B 10 N1 DG B 10 C2 -0.049 REMARK 500 1 DG B 10 N7 DG B 10 C8 0.042 REMARK 500 1 DG B 11 N7 DG B 11 C8 0.043 REMARK 500 1 DT B 12 C5 DT B 12 C6 0.045 REMARK 500 1 DT B 12 C6 DT B 12 N1 -0.046 REMARK 500 2 DC A 2 C5 DC A 2 C6 0.052 REMARK 500 2 DC A 3 N1 DC A 3 C6 -0.038 REMARK 500 2 DG A 4 N7 DG A 4 C8 0.043 REMARK 500 2 DG A 5 N7 DG A 5 C8 0.038 REMARK 500 2 DT A 6 C5 DT A 6 C6 0.045 REMARK 500 2 DT A 6 C6 DT A 6 N1 -0.045 REMARK 500 2 DC B 8 C5 DC B 8 C6 0.049 REMARK 500 2 DC B 9 N1 DC B 9 C6 -0.037 REMARK 500 2 DG B 10 N1 DG B 10 C2 -0.051 REMARK 500 2 DG B 10 N7 DG B 10 C8 0.042 REMARK 500 2 DG B 11 N7 DG B 11 C8 0.042 REMARK 500 2 DT B 12 C5 DT B 12 C6 0.046 REMARK 500 2 DT B 12 C6 DT B 12 N1 -0.046 REMARK 500 3 DC A 2 C5 DC A 2 C6 0.050 REMARK 500 3 DC A 3 N1 DC A 3 C6 -0.038 REMARK 500 3 DG A 4 N7 DG A 4 C8 0.044 REMARK 500 3 DG A 5 N7 DG A 5 C8 0.037 REMARK 500 3 DT A 6 C5 DT A 6 C6 0.046 REMARK 500 3 DT A 6 C6 DT A 6 N1 -0.045 REMARK 500 3 DG B 10 N1 DG B 10 C2 -0.048 REMARK 500 3 DG B 10 N7 DG B 10 C8 0.042 REMARK 500 3 DG B 11 N7 DG B 11 C8 0.043 REMARK 500 3 DT B 12 C5 DT B 12 C6 0.043 REMARK 500 3 DT B 12 C6 DT B 12 N1 -0.046 REMARK 500 4 DC A 3 N1 DC A 3 C6 -0.038 REMARK 500 4 DG A 4 N7 DG A 4 C8 0.040 REMARK 500 4 DG A 5 N7 DG A 5 C8 0.037 REMARK 500 4 DT A 6 C5 DT A 6 C6 0.046 REMARK 500 4 DT A 6 C6 DT A 6 N1 -0.045 REMARK 500 4 DC B 8 C4 DC B 8 C5 -0.049 REMARK 500 4 DC B 9 N1 DC B 9 C6 -0.037 REMARK 500 4 DG B 10 N7 DG B 10 C8 0.042 REMARK 500 4 DG B 11 N7 DG B 11 C8 0.043 REMARK 500 4 DT B 12 C5 DT B 12 C6 0.045 REMARK 500 4 DT B 12 C6 DT B 12 N1 -0.046 REMARK 500 5 DC A 2 C5 DC A 2 C6 0.051 REMARK 500 5 DC A 3 N1 DC A 3 C6 -0.043 REMARK 500 REMARK 500 THIS ENTRY HAS 120 BOND DEVIATIONS. 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 N1 - C2 - N3 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DA A 1 C2 - N3 - C4 ANGL. DEV. = 6.3 DEGREES REMARK 500 1 DA A 1 N3 - C4 - C5 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DA A 1 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC A 2 C2 - N3 - C4 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC A 2 N1 - C2 - O2 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DC A 3 N1 - C2 - O2 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DG A 4 C2 - N3 - C4 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DG A 4 N3 - C4 - C5 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DG A 4 C4 - C5 - N7 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DG A 4 C6 - C5 - N7 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DG A 5 C2 - N3 - C4 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 5 N3 - C4 - C5 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DG A 5 C4 - C5 - N7 ANGL. DEV. = -2.4 DEGREES REMARK 500 1 DG A 5 N3 - C4 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA B 7 N1 - C2 - N3 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DA B 7 C2 - N3 - C4 ANGL. DEV. = 6.2 DEGREES REMARK 500 1 DA B 7 N3 - C4 - C5 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DA B 7 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DC B 8 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DC B 8 C2 - N3 - C4 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DC B 8 N1 - C2 - O2 ANGL. DEV. = 5.5 DEGREES REMARK 500 1 DC B 9 N1 - C2 - O2 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DG B 10 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG B 10 C2 - N3 - C4 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG B 10 N3 - C4 - C5 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DG B 11 C2 - N3 - C4 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DG B 11 N3 - C4 - C5 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG B 11 C4 - C5 - N7 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 DA A 1 N1 - C2 - N3 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DA A 1 C2 - N3 - C4 ANGL. DEV. = 5.9 DEGREES REMARK 500 2 DA A 1 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DC A 2 C2 - N3 - C4 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DC A 2 N1 - C2 - O2 ANGL. DEV. = 5.5 DEGREES REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DG A 4 C2 - N3 - C4 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DG A 4 N3 - C4 - C5 ANGL. DEV. = -4.1 DEGREES REMARK 500 2 DG A 4 C4 - C5 - N7 ANGL. DEV. = -3.4 DEGREES REMARK 500 2 DG A 4 C6 - C5 - N7 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DG A 5 C2 - N3 - C4 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 DG A 5 N3 - C4 - C5 ANGL. DEV. = -5.8 DEGREES REMARK 500 2 DG A 5 N3 - C4 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DA B 7 N1 - C2 - N3 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 DA B 7 C2 - N3 - C4 ANGL. DEV. = 6.1 DEGREES REMARK 500 2 DA B 7 N3 - C4 - C5 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 DA B 7 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DC B 8 C2 - N3 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DC B 8 N1 - C2 - O2 ANGL. DEV. = 6.2 DEGREES REMARK 500 2 DC B 9 N1 - C2 - O2 ANGL. DEV. = 5.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 296 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 B 10 0.06 SIDE CHAIN REMARK 500 9 DG B 10 0.06 SIDE CHAIN REMARK 500 10 DG B 10 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEH A 13 DBREF 1JHI A 1 6 PDB 1JHI 1JHI 1 6 DBREF 1JHI B 7 12 PDB 1JHI 1JHI 7 12 SEQRES 1 A 6 DA DC DC DG DG DT SEQRES 1 B 6 DA DC DC DG DG DT HET HEH A 13 106 HETNAM HEH HEDAMYCIN FORMUL 3 HEH C41 H52 N2 O11 2+ LINK N7 DG A 4 C18 HEH A 13 1555 1555 1.48 SITE 1 AC1 4 DC A 3 DG A 4 DC B 9 DG B 10 CRYST1 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