Header list of 207d.pdb file
Complete list - 29 20 Bytes
HEADER DNA 20-APR-95 207D TITLE SOLUTION STRUCTURE OF MITHRAMYCIN DIMERS BOUND TO PARTIALLY TITLE 2 OVERLAPPING SITES ON DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*AP*GP*CP*TP*AP*GP*CP*TP*A)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS DNA, DOUBLE HELIX, MITHRAMYCIN EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR M.SASTRY,R.FIALA,D.J.PATEL REVDAT 4 29-JUL-20 207D 1 CAVEAT COMPND REMARK HETNAM REVDAT 4 2 1 LINK SITE ATOM REVDAT 3 24-JUN-20 207D 1 CAVEAT SOURCE REMARK DBREF REVDAT 3 2 1 LINK REVDAT 2 24-FEB-09 207D 1 VERSN REVDAT 1 15-SEP-95 207D 0 JRNL AUTH M.SASTRY,R.FIALA,D.J.PATEL JRNL TITL SOLUTION STRUCTURE OF MITHRAMYCIN DIMERS BOUND TO PARTIALLY JRNL TITL 2 OVERLAPPING SITES ON DNA. JRNL REF J.MOL.BIOL. V. 251 674 1995 JRNL REFN ISSN 0022-2836 JRNL PMID 7666419 JRNL DOI 10.1006/JMBI.1995.0464 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 STRUCTURES WERE OBTAINED REMARK 3 BY MANUALLY DOCKING MITHRAMYCIN 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 (40, 80, 120, 160, 250 MS NOESY EXPERIMENTS) AND DELTA REMARK 3 DIHEDRAL ANGLES DERIVED FROM SIMULATION OF COSY CROSS PEAK REMARK 3 PATTERNS. THE EIGHT DISTANCE RESTRAINED STRUCTURES WERE OBTAINED REMARK 3 BY TAKING THE AVERAGE COORDINATES OF THE LAST 2.0 PS OF THE REMARK 3 DYNAMICS DURING DISTANCE RESTRAINED DYNAMICS AND MINIMIZED. THE REMARK 3 RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE EIGHT FINAL REMARK 3 STRUCTURES ARE: BOND (ANG): MDL1 MDL2 MDL3 MDL4 MDL5 MDL6 MDL7 REMARK 3 MDL8 0.009 0.009 0.009 0.008 0.009 0.009 0.009 0.009 ANGLE (DEG): REMARK 3 MDL1 MDL2 MDL3 MDL4 MDL5 MDL6 MDL7 MDL8 2.627 2.630 2.631 2.636 REMARK 3 2.621 2.638 2.664 2.652 IMPROPER(DEG): MDL1 MDL2 MDL3 MDL4 MDL5 REMARK 3 MDL6 MDL7 MDL8 0.866 0.850 0.808 0.874 0.841 0.803 0.881 0.808 REMARK 4 REMARK 4 207D 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_1000177560. 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 REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 8 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 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: EACH MODEL CONTAINS FOUR MOLECULES OF MITHRAMYCIN (EACH REMARK 210 WITH FORMULA C52 H75 O24, CHARGE -1) AND TWO MG++ CATIONS THAT REMARK 210 COORDINATE TO TWO MITHRAMYCIN MOLECULES. IN THIS ENTRY REMARK 210 MITHRAMYCIN IS PRESENTED AS HET GROUPS DDA-DDA-CHR- TSC. THE TSC REMARK 210 RESIDUE IS COMPRISED OF THREE SACCHARIDE UNITS (DDA-DDL-MDA). REMARK 210 THE HYDROPHILIC SIDE CHAIN AND THE A-B DISACCHARIDE OF REMARK 210 MITHRAMYCIN MOLECULES ALONG WITH THE TERMINAL BASE PAIR IN THE REMARK 210 DNA DUPLEX ARE NOT WELL DEFINED. 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, G, H, I, J 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O1 DDA E 1 C6 CRH A 27 1.38 REMARK 500 O1 DDA H 1 C6 CRH B 17 1.38 REMARK 500 O1 DDA I 1 C6 CRH B 23 1.39 REMARK 500 O1 DDA C 1 C6 CRH A 13 1.39 REMARK 500 O1 DDA D 1 C2 CRH A 13 1.43 REMARK 500 O1 DDA J 1 C2 CRH B 23 1.43 REMARK 500 O1 DDA F 1 C2 CRH A 27 1.43 REMARK 500 O1 DDA G 1 C2 CRH B 17 1.43 REMARK 500 REMARK 500 REMARK: NULL 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 0.038 REMARK 500 1 DT B 1 C5 DT B 1 C7 0.040 REMARK 500 2 DT A 1 C5 DT A 1 C7 0.038 REMARK 500 2 DT B 1 C5 DT B 1 C7 0.038 REMARK 500 3 DT A 1 C5 DT A 1 C7 0.039 REMARK 500 3 DT A 9 C5 DT A 9 C7 0.037 REMARK 500 3 DT B 1 C5 DT B 1 C7 0.037 REMARK 500 4 DT A 1 C5 DT A 1 C7 0.038 REMARK 500 4 DT B 1 C5 DT B 1 C7 0.038 REMARK 500 5 DT A 1 C5 DT A 1 C7 0.038 REMARK 500 5 DT B 1 C5 DT B 1 C7 0.037 REMARK 500 6 DT A 1 C5 DT A 1 C7 0.037 REMARK 500 6 DT B 1 C5 DT B 1 C7 0.037 REMARK 500 7 DT A 1 C5 DT A 1 C7 0.037 REMARK 500 7 DT B 1 C5 DT B 1 C7 0.038 REMARK 500 8 DT A 1 C5 DT A 1 C7 0.039 REMARK 500 8 DT B 1 C5 DT B 1 C7 0.038 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 2 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DC A 4 O4' - C1' - N1 ANGL. DEV. = 7.4 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DC A 8 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DT A 9 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DA A 10 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DA B 2 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DG B 3 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DC B 4 O4' - C1' - N1 ANGL. DEV. = 7.4 DEGREES REMARK 500 1 DT B 5 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DC B 8 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DT B 9 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DA B 10 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 2 DG A 3 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 2 DG A 3 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 2 DC A 4 O4' - C1' - N1 ANGL. DEV. = 7.3 DEGREES REMARK 500 2 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DC A 8 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DT A 9 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 2 DG B 3 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 2 DG B 3 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 2 DC B 4 O4' - C1' - N1 ANGL. DEV. = 7.2 DEGREES REMARK 500 2 DT B 5 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DC B 8 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DT B 9 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 3 DT A 1 C3' - O3' - P ANGL. DEV. = 8.3 DEGREES REMARK 500 3 DG A 3 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 3 DC A 4 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 3 DC A 8 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 3 DT A 9 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 3 DA A 10 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 3 DT B 1 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 3 DG B 3 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 3 DC B 4 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 3 DC B 8 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 3 DT B 9 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 3 DA B 10 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 4 DG A 3 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 4 DG A 3 O4' - C1' - N9 ANGL. DEV. = 6.6 DEGREES REMARK 500 4 DC A 4 O4' - C1' - N1 ANGL. DEV. = 7.5 DEGREES REMARK 500 4 DT A 5 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 4 DC A 8 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 4 DT A 9 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 4 DG B 3 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 4 DG B 3 O4' - C1' - N9 ANGL. DEV. = 6.6 DEGREES REMARK 500 4 DC B 4 O4' - C1' - N1 ANGL. DEV. = 7.5 DEGREES REMARK 500 4 DT B 5 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 4 DC B 8 C4' - C3' - C2' ANGL. DEV. = -4.2 DEGREES REMARK 500 4 DC B 8 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 99 ANGLE DEVIATIONS. 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 19 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CRH A 13 O1 REMARK 620 2 CRH A 13 O9 78.5 REMARK 620 3 CRH B 17 O1 72.8 104.1 REMARK 620 4 CRH B 17 O9 99.9 178.0 74.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 29 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CRH A 27 O1 REMARK 620 2 CRH A 27 O9 74.3 REMARK 620 3 CRH B 23 O1 72.7 99.7 REMARK 620 4 CRH B 23 O9 104.0 177.9 78.5 REMARK 620 N 1 2 3 DBREF 207D A 1 10 PDB 207D 207D 1 10 DBREF 207D B 1 10 PDB 207D 207D 1 10 SEQRES 1 A 10 DT DA DG DC DT DA DG DC DT DA SEQRES 1 B 10 DT DA DG DC DT DA DG DC DT 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 DDA G 1 20 HET DDL G 2 19 HET MDA G 3 23 HET DDA H 1 20 HET DDA H 2 20 HET DDA I 1 20 HET DDA I 2 20 HET DDA J 1 20 HET DDL J 2 19 HET MDA J 3 23 HET MG A 19 1 HET CRH A 13 49 HET CRH A 27 49 HET MG B 29 1 HET CRH B 17 49 HET CRH B 23 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 2,6-DIDEOXY-BETA-D-MANNOSE HETSYN DDL 2,6-DIDEOXY-BETA-D-TALOSE FORMUL 3 DDA 12(C6 H12 O4) FORMUL 4 DDL 4(C6 H12 O4) FORMUL 4 MDA 4(C7 H14 O4) FORMUL 11 MG 2(MG 2+) FORMUL 12 CRH 4(C21 H24 O7) LINK O3 DDA C 1 C1 DDA C 2 1555 1555 1.43 LINK O3 DDA D 1 C1 DDL D 2 1555 1555 1.42 LINK O3 DDL D 2 C1 MDA D 3 1555 1555 1.41 LINK O3 DDA E 1 C1 DDA E 2 1555 1555 1.43 LINK O3 DDA F 1 C1 DDL F 2 1555 1555 1.44 LINK O3 DDL F 2 C1 MDA F 3 1555 1555 1.42 LINK O3 DDA G 1 C1 DDL G 2 1555 1555 1.44 LINK O3 DDL G 2 C1 MDA G 3 1555 1555 1.42 LINK O3 DDA H 1 C1 DDA H 2 1555 1555 1.43 LINK O3 DDA I 1 C1 DDA I 2 1555 1555 1.43 LINK O3 DDA J 1 C1 DDL J 2 1555 1555 1.42 LINK O3 DDL J 2 C1 MDA J 3 1555 1555 1.41 LINK O1 CRH A 13 MG MG A 19 1555 1555 2.29 LINK O9 CRH A 13 MG MG A 19 1555 1555 1.80 LINK MG MG A 19 O1 CRH B 17 1555 1555 2.29 LINK MG MG A 19 O9 CRH B 17 1555 1555 1.91 LINK O1 CRH A 27 MG MG B 29 1555 1555 2.29 LINK O9 CRH A 27 MG MG B 29 1555 1555 1.91 LINK O1 CRH B 23 MG MG B 29 1555 1555 2.29 LINK O9 CRH B 23 MG MG B 29 1555 1555 1.80 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
Complete list - 29 20 Bytes