HEADER DNA 01-DEC-94 199D TITLE SOLUTION STRUCTURE OF THE MONOALKYLATED MITOMYCIN C-DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*(DI)P*CP*AP*CP*GP*TP*CP*(DI)P*T)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*AP*CP*GP*AP*CP*GP*TP*GP*C)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS DNA, MITOMYCIN, DOUBLE HELIX EXPDTA SOLUTION NMR NUMMDL 3 AUTHOR M.SASTRY,R.FIALA,R.LIPMAN,M.TOMASZ,D.J.PATEL REVDAT 4 13-MAR-24 199D 1 COMPND SOURCE REVDAT 3 16-FEB-22 199D 1 REMARK LINK REVDAT 2 24-FEB-09 199D 1 VERSN REVDAT 1 07-FEB-95 199D 0 JRNL AUTH M.SASTRY,R.FIALA,R.LIPMAN,M.TOMASZ,D.J.PATEL JRNL TITL SOLUTION STRUCTURE OF THE MONOALKYLATED MITOMYCIN C-DNA JRNL TITL 2 COMPLEX. JRNL REF J.MOL.BIOL. V. 247 338 1995 JRNL REFN ISSN 0022-2836 JRNL PMID 7707379 JRNL DOI 10.1006/JMBI.1994.0143 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: THREE STARTING STRUCTURES WERE OBTAINED REMARK 3 BY MANUALLY DOCKING MITOMYCIN C ON A FORM AND B FORM DNA. THESE REMARK 3 WERE SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR REMARK 3 DYNAMICS USING A SET OF INTER-PROTON DISTANCES DERIVED FROM NMR REMARK 3 DATA. THE THREE DISTANCE-REFINED STRUCTURES WERE REFINED FURTHER REMARK 3 USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR REMARK 3 DYNAMICS. THE FINAL THREE STRUCTURES WERE OBTAINED BY TAKING THE REMARK 3 AVERAGE COORDINATES OF THE LAST 1.5 PS OF THE DYNAMICS DURING REMARK 3 RELAXATION MATRIX REFINEMENT AND MINIMIZED. THE R(1/6) VALUE WAS REMARK 3 USED TO REFINE THE STRUCTURE DURING RELAXATION MATRIX REMARK 3 REFINEMENT. THE SUMMATIONS RUN THROUGH OBSERVED, QUANTIFIABLE REMARK 3 NOE CROSSPEAKS IN NOESY SPECTRA RECORDED IN D2O AND MIXING TIMES REMARK 3 OF 30, 60, 90, 120, 200 AND 300 MS. THE R(1/6) FACTOR AND THE REMARK 3 RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE THREE FINAL REMARK 3 STRUCTURES ARE: MDL1 MDL2 MDL3 R(1/6) FACTOR 0.027 0.026 0.026 REMARK 3 BOND (ANG) 0.008 0.008 0.008 ANGLE (DEG) 2.913 2.931 2.949 REMARK 3 IMPROPER (DEG) 0.361 0.393 0.372 REMARK 4 REMARK 4 199D 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_1000170219. 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 : 3 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 3 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: 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: 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 DT A 6 C5 DT A 6 C7 0.040 REMARK 500 1 DT A 9 C5 DT A 9 C7 0.038 REMARK 500 2 DT A 6 C5 DT A 6 C7 0.042 REMARK 500 2 DT A 9 C5 DT A 9 C7 0.039 REMARK 500 3 DT A 6 C5 DT A 6 C7 0.044 REMARK 500 3 DT A 9 C5 DT A 9 C7 0.042 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 DC A 2 O4' - C4' - C3' ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC A 2 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DC A 2 C3' - O3' - P ANGL. DEV. = 10.4 DEGREES REMARK 500 1 DA A 3 O4' - C1' - N9 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DA A 3 C3' - O3' - P ANGL. DEV. = 9.1 DEGREES REMARK 500 1 DC A 4 C4' - C3' - C2' ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DC A 4 O4' - C1' - C2' ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DC A 4 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 5 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 1 DC A 7 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DA B 10 C1' - O4' - C4' ANGL. DEV. = -9.1 DEGREES REMARK 500 1 DA B 10 O4' - C1' - C2' ANGL. DEV. = -6.0 DEGREES REMARK 500 1 DA B 10 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 DG B 12 C5' - C4' - O4' ANGL. DEV. = 6.7 DEGREES REMARK 500 1 DG B 12 O4' - C1' - C2' ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DG B 12 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 DC B 14 O4' - C1' - N1 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DC B 14 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG B 15 C5' - C4' - O4' ANGL. DEV. = 7.1 DEGREES REMARK 500 1 DG B 15 O4' - C1' - C2' ANGL. DEV. = -6.9 DEGREES REMARK 500 1 DG B 15 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT B 16 O4' - C1' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DT B 16 O4' - C1' - N1 ANGL. DEV. = 8.7 DEGREES REMARK 500 1 DG B 17 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 1 DC B 18 C4' - C3' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DC B 18 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 2 DC A 2 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DC A 2 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 2 DC A 4 O4' - C1' - C2' ANGL. DEV. = -7.9 DEGREES REMARK 500 2 DC A 4 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 DC A 4 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DG A 5 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES REMARK 500 2 DG A 5 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 2 DT A 6 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 DC A 7 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DA B 10 C1' - O4' - C4' ANGL. DEV. = -9.3 DEGREES REMARK 500 2 DA B 10 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 2 DA B 10 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 2 DA B 10 C3' - O3' - P ANGL. DEV. = 8.8 DEGREES REMARK 500 2 DG B 12 C5' - C4' - O4' ANGL. DEV. = 8.3 DEGREES REMARK 500 2 DG B 12 O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES REMARK 500 2 DG B 12 C3' - O3' - P ANGL. DEV. = 10.5 DEGREES REMARK 500 2 DG B 15 O4' - C1' - C2' ANGL. DEV. = -6.2 DEGREES REMARK 500 2 DG B 15 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DT B 16 O4' - C1' - N1 ANGL. DEV. = 12.1 DEGREES REMARK 500 2 DG B 17 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 DC B 18 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DI A 1 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 74 ANGLE DEVIATIONS. 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 MOC A 19 DBREF 199D A 1 9 PDB 199D 199D 1 9 DBREF 199D B 10 18 PDB 199D 199D 10 18 SEQRES 1 A 9 DI DC DA DC DG DT DC DI DT SEQRES 1 B 9 DA DC DG DA DC DG DT DG DC HET MOC A 19 37 HETNAM MOC CARBAMIC ACID 2,6-DIAMINO-5-METHYL-4,7-DIOXO-2,3,4,7- HETNAM 2 MOC TETRAHYDRO-1H-3A-AZA-CYCLOPENTA[A]INDEN-8-YLMETHYL HETNAM 3 MOC ESTER FORMUL 3 MOC C14 H16 N4 O4 LINK N2 DG A 5 C1 MOC A 19 1555 1555 1.43 SITE 1 AC1 6 DG A 5 DT A 6 DC A 7 DC B 14 SITE 2 AC1 6 DG B 15 DT B 16 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