HEADER DNA 09-NOV-93 146D TITLE SOLUTION STRUCTURE OF THE MITHRAMYCIN DIMER-DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*CP*GP*CP*GP*A)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS DNA, MITHRAMYCIN DIMER EXPDTA SOLUTION NMR NUMMDL 2 AUTHOR M.SASTRY,D.J.PATEL REVDAT 7 22-MAY-24 146D 1 REMARK REVDAT 6 19-JAN-22 146D 1 COMPND HETSYN REVDAT 5 29-JUL-20 146D 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE ATOM REVDAT 4 09-JUN-09 146D 1 REVDAT REVDAT 3 07-APR-09 146D 1 REMARK REVDAT 2 24-FEB-09 146D 1 VERSN REVDAT 1 31-MAR-95 146D 0 JRNL AUTH M.SASTRY,D.J.PATEL JRNL TITL SOLUTION STRUCTURE OF THE MITHRAMYCIN DIMER-DNA COMPLEX. JRNL REF BIOCHEMISTRY V. 32 6588 1993 JRNL REFN ISSN 0006-2960 JRNL PMID 8329387 JRNL DOI 10.1021/BI00077A012 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: TWO STARTING MODELS WERE OBTAINED BY REMARK 3 DOCKING THE MG2+ COORDINATED MITHRAMYCIN DIMER IN THE MINOR REMARK 3 GROOVE OF A AND B FORM D(TCGCGA) DUPLEX. THESE MODELS WERE REMARK 3 SUBSEQUENTLY REFINED BY DISTANCE RESTRAINED MOLECULAR DYNAMICS REMARK 3 USING A SET OF INTER-PROTON DISTANCE RESTRAINTS DERIVED FROM THE REMARK 3 NMR DATA. THE TWO DISTANCE-REFINED STRUCTURES WERE REFINED REMARK 3 FURTHER USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED REMARK 3 MOLECULAR DYNAMICS. THE FINAL TWO STRUCTURES WERE OBTAINED BY REMARK 3 TAKING THE AVERAGE COORDINATES OF THE LAST 1 PS OF THE DYNAMICS REMARK 3 DURING RELAXATION MATRIX REFINEMENT AND MINIMIZED. THE R VALUE REMARK 3 WAS USED TO REFINE THE STRUCTURE DURING RELAXATION MATRIX REMARK 3 REFINEMENT. THE R FACTOR AND THE RMS DEVIATIONS FROM IDEAL REMARK 3 GEOMETRY FOR THE TWO FINAL STRUCTURES ARE: MODEL 1 MODEL 2 R REMARK 3 FACTOR 0.146 0.136 BOND (ANGSTROMS) 0.016 0.013 ANGLES (DEGREES) REMARK 3 3.410 3.369. THE STRUCTURE EXHIBITS APPROXIMATE TWO-FOLD REMARK 3 SYMMETRY, PERPENDICULAR TO THE HELICAL AXIS AND PASSING THROUGH REMARK 3 THE MAGNESIUM IN THE COMPLEX. THE TRANSFORMATION PRESENTED ON * REMARK 3 MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR REMARK 3 CHAIN B OF MODEL 1 WHEN APPLIED TO CHAIN A OF MODEL 1. THE REMARK 3 TRANSFORMATION PRESENTED ON *MTRIX 2* RECORDS BELOW WILL YIELD REMARK 3 APPROXIMATE COORDINATES FOR CHAIN B OF MODEL 2 WHEN APPLIED TO REMARK 3 CHAIN A OF MODEL 2. REMARK 4 REMARK 4 146D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170106. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : MOLECULAR DYNAMICS, MATRIX REMARK 210 RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 2 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 2 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE HYDROXYL PROTONS IN THE RELAXATION MATRIX REFINED REMARK 210 STRUCTURES ARE NOT WELL DETERMINED. THE HYDROPHILIC SIDE CHAIN, REMARK 210 THE B SUGAR RESIDUE DDA 1 AND DDA 7, AND RESIDUES T 1 AND C 2 REMARK 210 ARE UNDETERMINED. 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, C, D, E, F 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 1 C5 DT A 1 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 DT A 1 O4' - C1' - N1 ANGL. DEV. = 6.3 DEGREES REMARK 500 1 DC A 2 O4' - C1' - N1 ANGL. DEV. = 7.5 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG A 3 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG A 3 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DC A 4 C4' - C3' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DC A 4 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DG A 5 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DA A 6 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT B 7 O4' - C1' - N1 ANGL. DEV. = 6.3 DEGREES REMARK 500 1 DC B 8 O4' - C1' - N1 ANGL. DEV. = 7.5 DEGREES REMARK 500 1 DG B 9 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG B 9 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG B 9 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DC B 10 C4' - C3' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DC B 10 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DG B 11 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DA B 12 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DT A 1 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 2 DT A 1 C3' - O3' - P ANGL. DEV. = 9.2 DEGREES REMARK 500 2 DC A 2 O4' - C1' - N1 ANGL. DEV. = 8.4 DEGREES REMARK 500 2 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DG A 3 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DG A 3 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 DC A 4 C4' - C3' - C2' ANGL. DEV. = -5.7 DEGREES REMARK 500 2 DC A 4 O4' - C1' - N1 ANGL. DEV. = 6.5 DEGREES REMARK 500 2 DG A 5 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DA A 6 C5' - C4' - O4' ANGL. DEV. = 9.6 DEGREES REMARK 500 2 DA A 6 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 DT B 7 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 2 DT B 7 C3' - O3' - P ANGL. DEV. = 9.1 DEGREES REMARK 500 2 DC B 8 O4' - C1' - N1 ANGL. DEV. = 8.5 DEGREES REMARK 500 2 DG B 9 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DG B 9 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DG B 9 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 DC B 10 C4' - C3' - C2' ANGL. DEV. = -5.6 DEGREES REMARK 500 2 DC B 10 O4' - C1' - N1 ANGL. DEV. = 6.5 DEGREES REMARK 500 2 DG B 11 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DA B 12 C5' - C4' - O4' ANGL. DEV. = 9.7 DEGREES REMARK 500 2 DA B 12 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES 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 DC A 4 0.07 SIDE CHAIN REMARK 500 1 DA A 6 0.06 SIDE CHAIN REMARK 500 1 DC B 10 0.07 SIDE CHAIN REMARK 500 1 DA B 12 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 13 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CRH A 9 O9 REMARK 620 2 CRH A 9 O1 70.2 REMARK 620 3 CRH B 3 O9 179.8 109.8 REMARK 620 4 CRH B 3 O1 110.0 80.4 70.3 REMARK 620 N 1 2 3 DBREF 146D A 1 6 PDB 146D 146D 1 6 DBREF 146D B 7 12 PDB 146D 146D 7 12 SEQRES 1 A 6 DT DC DG DC DG DA SEQRES 1 B 6 DT DC DG DC DG DA HET DDA C 1 20 HET DDA C 2 20 HET DDA D 1 20 HET DDL D 2 19 HET MDA D 3 23 HET DDA E 1 20 HET DDA E 2 20 HET DDA F 1 20 HET DDL F 2 19 HET MDA F 3 23 HET MG A 13 1 HET CRH A 9 49 HET CRH B 3 49 HETNAM DDA BETA-D-OLIVOPYRANOSE HETNAM DDL 2,6-DIDEOXY-BETA-D-GALACTOPYRANOSE HETNAM MDA 2,6-DIDEOXY-3-C-METHYL-BETA-D-RIBO-HEXOPYRANOSE HETNAM MG MAGNESIUM ION HETNAM CRH 1,2-HYDRO-1-OXY-3,4-HYDRO-3-(1-METHOXY-2-OXY-3,4- HETNAM 2 CRH DIHYDROXYPENTYL)-8,9-DIHYROXY-7-METHYLANTHRACENE HETSYN DDA BETA-D-OLIVOSE; 2,6-DIDEOXY-BETA-D-ARABINO- HETSYN 2 DDA HEXOPYRANOSE; 2,6-DIDEOXY-BETA-D-GLUCOPYRANOSE; 2,6- HETSYN 3 DDA DIDEOXY-BETA-D-MANNOPYRANOSE; 2-DEOXY-BETA-D- HETSYN 4 DDA QUINOVOPYRANOSE; 2-DEOXY-BETA-D-RHAMNOOPYRANOSE; D- HETSYN 5 DDA OLIVOSE; OLIVOSE; 2,6-DIDEOXY-BETA-D-GLUCOSE; 2,6- HETSYN 6 DDA DIDEOXY-BETA-D-MANNOSE HETSYN DDL 2,6-DIDEOXY-BETA-D-GALACTOSE; 2,6-DIDEOXY-BETA-D- HETSYN 2 DDL TALOSE; 2,6-DIDEOXY-BETA-D-LYXO-HEXOPYRANOSE; 2-DEOXY- HETSYN 3 DDL BETA-D-FUCOPYRANOSE; 2,6-DIDEOXY-D-GALACTOSE; 2,6- HETSYN 4 DDL DIDEOXY-GALACTOSE HETSYN MDA 2,6-DIDEOXY-3 C-METHYL-D-RIBOPYRANOSIDE; 2,6-DIDEOXY-3- HETSYN 2 MDA C-METHYL-BETA-D-RIBO-HEXOSE; 2,6-DIDEOXY-3-C-METHYL-D- HETSYN 3 MDA RIBO-HEXOSE; 2,6-DIDEOXY-3-C-METHYL-RIBO-HEXOSE FORMUL 3 DDA 6(C6 H12 O4) FORMUL 4 DDL 2(C6 H12 O4) FORMUL 4 MDA 2(C7 H14 O4) FORMUL 7 MG MG 2+ FORMUL 8 CRH 2(C21 H24 O7) LINK C6 CRH A 9 O1 DDA C 1 1555 1555 1.39 LINK C2 CRH A 9 O1 DDA D 1 1555 1555 1.43 LINK C6 CRH B 3 O1 DDA E 1 1555 1555 1.39 LINK C2 CRH B 3 O1 DDA F 1 1555 1555 1.43 LINK O3 DDA C 1 C1 DDA C 2 1555 1555 1.43 LINK O3 DDA D 1 C1 DDL D 2 1555 1555 1.43 LINK O3 DDL D 2 C1 MDA D 3 1555 1555 1.44 LINK O3 DDA E 1 C1 DDA E 2 1555 1555 1.43 LINK O3 DDA F 1 C1 DDL F 2 1555 1555 1.43 LINK O3 DDL F 2 C1 MDA F 3 1555 1555 1.44 LINK O9 CRH A 9 MG MG A 13 1555 1555 2.13 LINK O1 CRH A 9 MG MG A 13 1555 1555 2.38 LINK MG MG A 13 O9 CRH B 3 1555 1555 2.13 LINK MG MG A 13 O1 CRH B 3 1555 1555 2.38 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