Header list of 146d.pdb file
Complete list - 19 20 Bytes
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 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
Complete list - 19 20 Bytes