10 20 30 40 50 60 70 80 146D - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER 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, NMR, MITHRAMYCIN DIMER
EXPDTA SOLUTION NMR
NUMMDL 2
AUTHOR M.SASTRY,D.J.PATEL
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 JRNL TITL 2 COMPLEX. JRNL REF BIOCHEMISTRY V. 32 6588 1993 JRNL REFN ISSN 0006-2960 JRNL PMID 8329387 JRNL DOI 10.1021/BI00077A012
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 2.1 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 REMARK 3 THE 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 REMARK 3 DYNAMICS DURING RELAXATION MATRIX REFINEMENT AND MINIMIZED. REMARK 3 THE R VALUE WAS USED TO REFINE THE STRUCTURE DURING RELAXATION REMARK 3 MATRIX REFINEMENT. THE R FACTOR AND THE RMS DEVIATIONS FROM REMARK 3 IDEAL GEOMETRY FOR THE TWO FINAL STRUCTURES ARE: MODEL 1 MODEL REMARK 3 2 R FACTOR 0.146 0.136 BOND (ANGSTROMS) 0.016 0.013 ANGLES REMARK 3 (DEGREES) 3.410 3.369. THE STRUCTURE EXHIBITS APPROXIMATE TWO- REMARK 3 FOLD SYMMETRY, PERPENDICULAR TO THE HELICAL AXIS AND PASSING REMARK 3 THROUGH THE MAGNESIUM IN THE COMPLEX. THE TRANSFORMATION REMARK 3 PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE REMARK 3 COORDINATES FOR CHAIN B OF MODEL 1 WHEN APPLIED TO CHAIN A OF REMARK 3 MODEL 1. THE TRANSFORMATION PRESENTED ON *MTRIX 2* RECORDS REMARK 3 BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN B OF MODEL REMARK 3 2 WHEN APPLIED TO 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 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 REMARK 210 CHAIN, THE B SUGAR RESIDUE DDA 1 AND DDA 7, AND RESIDUES T 1 REMARK 210 AND C 2 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 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 DC A 2 O4' - C1' - N1 ANGL. DEV. = 8.5 DEGREES REMARK 500 2 DT A 1 C3' - O3' - P ANGL. DEV. = 9.2 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 DC B 8 O4' - C1' - N1 ANGL. DEV. = 8.5 DEGREES REMARK 500 2 DT B 7 C3' - O3' - P ANGL. DEV. = 9.1 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 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 1 DDA B 2 REMARK 610 1 DDA B 4 REMARK 610 1 DDL B 5 REMARK 610 1 DDA A 8 REMARK 610 1 DDA A 10 REMARK 610 1 DDL A 11 REMARK 610 2 DDA B 2 REMARK 610 2 DDA B 4 REMARK 610 2 DDL B 5 REMARK 610 2 DDA A 8 REMARK 610 2 DDA A 10 REMARK 610 2 DDL A 11
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 1 MG A 13 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CRH B 3 O9 REMARK 620 2 CRH A 9 O9 179.8 REMARK 620 3 CRH B 3 O1 70.3 110.0 REMARK 620 4 CRH A 9 O1 109.8 70.2 80.4 REMARK 620 N 1 2 3
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CRH B 3 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CRH A 9 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDA B 1 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDA B 2 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDA B 4 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDA A 8 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDA A 10 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDA A 7 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDL B 5 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDL A 11 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MDA B 6 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MDA A 12 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 13
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 B 1 21 HET DDA B 2 19 HET DDA B 4 19 HET DDL B 5 19 HET DDA A 7 21 HET DDA A 8 19 HET DDA A 10 19 HET DDL A 11 19 HET MG A 13 1 HET CRH B 3 49 HET MDA B 6 24 HET CRH A 9 49 HET MDA A 12 24
HETNAM DDA 2,6-DIDEOXY-BETA-D-GLUCOSE HETNAM DDL 2,6-DIDEOXY-BETA-D-GALACTOSE 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 HETNAM MDA 2,6-DIDEOXY-3 C-METHYL-D-RIBOPYRANOSIDE
HETSYN DDA 2,6-DIDEOXY-BETA-D-MANNOSE HETSYN DDL 2,6-DIDEOXY-BETA-D-TALOSE
FORMUL 3 DDA 6(C6 H12 O4) FORMUL 4 DDL 2(C6 H12 O4) FORMUL 7 MG MG 2+ FORMUL 8 CRH 2(C21 H24 O7) FORMUL 9 MDA 2(C7 H14 O4)
LINK C3 DDA B 4 O1 DDL B 5 1555 1555 1.44 LINK C3 DDA A 10 O1 DDL A 11 1555 1555 1.44 LINK O1 DDA A 7 C3 DDA A 8 1555 1555 1.44 LINK C3 DDA B 2 O1 DDA B 1 1555 1555 1.44 LINK O1 DDA A 8 C6 CRH A 9 1555 1555 1.39 LINK C2 CRH A 9 O1 DDA A 10 1555 1555 1.43 LINK C3 DDL A 11 O1 MDA A 12 1555 1555 1.44 LINK MG MG A 13 O9 CRH B 3 1555 1555 2.13 LINK MG MG A 13 O9 CRH A 9 1555 1555 2.13 LINK MG MG A 13 O1 CRH B 3 1555 1555 2.38 LINK MG MG A 13 O1 CRH A 9 1555 1555 2.38 LINK O1 DDA B 2 C6 CRH B 3 1555 1555 1.39 LINK C2 CRH B 3 O1 DDA B 4 1555 1555 1.43 LINK C3 DDL B 5 O1 MDA B 6 1555 1555 1.44
SITE 1 AC1 5 DDA B 2 DDA B 4 MG A 13 DG B 9 SITE 2 AC1 5 DC B 10 SITE 1 AC2 5 DDA A 8 DDA A 10 MG A 13 DG A 3 SITE 2 AC2 5 DC A 4 SITE 1 AC3 2 DDA B 2 DG B 9 SITE 1 AC4 3 DDA B 1 CRH B 3 DDL A 11 SITE 1 AC5 4 CRH B 3 DDL B 5 DG B 11 DA B 12 SITE 1 AC6 2 DDA A 7 CRH A 9 SITE 1 AC7 4 CRH A 9 DDL A 11 DG A 5 DA A 6 SITE 1 AC8 2 DDA A 8 DG A 3 SITE 1 AC9 3 DDA B 4 MDA B 6 DA B 12 SITE 1 AD1 4 DDA B 2 DDA A 10 MDA A 12 DA A 6 SITE 1 AD2 3 DDL B 5 DG B 11 DA B 12 SITE 1 AD3 3 DDL A 11 DG A 5 DA A 6 SITE 1 AD4 2 CRH B 3 CRH A 9
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