PDB Short entry for 1D83 HEADER DNA 22-JUL-92 1D83 TITLE STRUCTURE REFINEMENT OF THE CHROMOMYCIN DIMER/DNA OLIGOMER COMPLEX IN TITLE 2 SOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*AP*AP*GP*GP*CP*CP*TP*T)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALY SYNTHESIZED KEYWDS DNA, DOUBLE HELIX, CHROMOMYCIN EXPDTA SOLUTION NMR AUTHOR X.GAO,P.MIRAU,D.J.PATEL REVDAT 5 02-AUG-23 1D83 1 HETSYN LINK ATOM REVDAT 4 29-JUL-20 1D83 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 24-FEB-09 1D83 1 VERSN REVDAT 2 01-APR-03 1D83 1 JRNL REVDAT 1 15-JUL-93 1D83 0 JRNL AUTH X.L.GAO,P.MIRAU,D.J.PATEL JRNL TITL STRUCTURE REFINEMENT OF THE CHROMOMYCIN DIMER-DNA OLIGOMER JRNL TITL 2 COMPLEX IN SOLUTION. JRNL REF J.MOL.BIOL. V. 223 259 1992 JRNL REFN ISSN 0022-2836 JRNL PMID 1731073 JRNL DOI 10.1016/0022-2836(92)90730-8 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: NULL REMARK 4 REMARK 4 1D83 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172681. 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 : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: CHROMOMYCIN BINDS AS A MG2 CATION-COORDINATED DIMER. EACH REMARK 210 CHROMOMYCIN IS REPRESENTED AS A SET OF SIX HET GROUPS: 1GL - ARI REMARK 210 - CPH - CDR - CDR - ERI. THE COORDINATING MG IS PRESENTED AS A REMARK 210 SEPARATE HET GROUP. 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: 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 H22 DG B 14 HO8 CPH B 23 1.19 REMARK 500 H22 DG A 4 HO8 CPH A 33 1.20 REMARK 500 H22 DG A 4 O8 CPH A 33 1.56 REMARK 500 H22 DG B 14 O8 CPH B 23 1.56 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 DA A 1 C5' DA A 1 C4' 0.046 REMARK 500 DA A 1 C2' DA A 1 C1' 0.085 REMARK 500 DA A 1 O4' DA A 1 C1' 0.066 REMARK 500 DA A 1 O4' DA A 1 C4' 0.054 REMARK 500 DA A 1 C6 DA A 1 N1 -0.048 REMARK 500 DA A 1 C8 DA A 1 N9 -0.079 REMARK 500 DA A 1 N9 DA A 1 C4 0.045 REMARK 500 DA A 2 C5' DA A 2 C4' 0.043 REMARK 500 DA A 2 C5 DA A 2 N7 0.039 REMARK 500 DA A 2 N9 DA A 2 C4 0.048 REMARK 500 DG A 3 C4' DG A 3 C3' 0.074 REMARK 500 DG A 3 C2' DG A 3 C1' 0.172 REMARK 500 DG A 3 O3' DG A 4 P 0.081 REMARK 500 DG A 4 P DG A 4 O5' 0.087 REMARK 500 DG A 4 C4' DG A 4 C3' 0.060 REMARK 500 DG A 4 N3 DG A 4 C4 0.134 REMARK 500 DG A 4 C5 DG A 4 N7 0.040 REMARK 500 DG A 4 C8 DG A 4 N9 0.049 REMARK 500 DG A 4 N9 DG A 4 C4 0.088 REMARK 500 DC A 5 C5' DC A 5 C4' 0.058 REMARK 500 DC A 6 C5' DC A 6 C4' 0.063 REMARK 500 DC A 6 O4' DC A 6 C1' 0.073 REMARK 500 DC A 6 O4' DC A 6 C4' 0.058 REMARK 500 DT A 7 C5' DT A 7 C4' 0.125 REMARK 500 DT A 7 C3' DT A 7 C2' 0.082 REMARK 500 DT A 7 O4' DT A 7 C1' 0.067 REMARK 500 DT A 7 C4 DT A 7 C5 0.056 REMARK 500 DT A 7 C5 DT A 7 C7 0.147 REMARK 500 DA B 11 C5' DA B 11 C4' 0.045 REMARK 500 DA B 11 C2' DA B 11 C1' 0.084 REMARK 500 DA B 11 O4' DA B 11 C1' 0.066 REMARK 500 DA B 11 O4' DA B 11 C4' 0.054 REMARK 500 DA B 11 C6 DA B 11 N1 -0.049 REMARK 500 DA B 11 C8 DA B 11 N9 -0.078 REMARK 500 DA B 11 N9 DA B 11 C4 0.043 REMARK 500 DA B 12 C5' DA B 12 C4' 0.047 REMARK 500 DA B 12 C5 DA B 12 C6 0.054 REMARK 500 DA B 12 C5 DA B 12 N7 0.038 REMARK 500 DA B 12 N9 DA B 12 C4 0.046 REMARK 500 DG B 13 C4' DG B 13 C3' 0.075 REMARK 500 DG B 13 C2' DG B 13 C1' 0.165 REMARK 500 DG B 13 O3' DG B 14 P 0.081 REMARK 500 DG B 14 P DG B 14 O5' 0.088 REMARK 500 DG B 14 C4' DG B 14 C3' 0.082 REMARK 500 DG B 14 N3 DG B 14 C4 0.137 REMARK 500 DG B 14 C5 DG B 14 N7 0.040 REMARK 500 DG B 14 N9 DG B 14 C4 0.088 REMARK 500 DC B 15 C5' DC B 15 C4' 0.055 REMARK 500 DC B 16 C5' DC B 16 C4' 0.065 REMARK 500 DC B 16 O4' DC B 16 C1' 0.070 REMARK 500 REMARK 500 THIS ENTRY HAS 55 BOND DEVIATIONS. 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 DA A 1 C1' - O4' - C4' ANGL. DEV. = 5.2 DEGREES REMARK 500 DA A 1 O4' - C1' - C2' ANGL. DEV. = -8.7 DEGREES REMARK 500 DA A 1 O4' - C1' - N9 ANGL. DEV. = 14.8 DEGREES REMARK 500 DA A 1 N1 - C2 - N3 ANGL. DEV. = 4.5 DEGREES REMARK 500 DA A 1 C5 - N7 - C8 ANGL. DEV. = -5.4 DEGREES REMARK 500 DA A 1 N7 - C8 - N9 ANGL. DEV. = 11.7 DEGREES REMARK 500 DA A 1 C8 - N9 - C4 ANGL. DEV. = -7.3 DEGREES REMARK 500 DA A 1 C4 - N9 - C1' ANGL. DEV. = 11.8 DEGREES REMARK 500 DA A 2 C5' - C4' - O4' ANGL. DEV. = 7.5 DEGREES REMARK 500 DA A 2 C4' - C3' - O3' ANGL. DEV. = -23.9 DEGREES REMARK 500 DA A 2 N9 - C1' - C2' ANGL. DEV. = 8.7 DEGREES REMARK 500 DA A 2 O4' - C1' - N9 ANGL. DEV. = 13.5 DEGREES REMARK 500 DA A 2 N1 - C6 - N6 ANGL. DEV. = -6.0 DEGREES REMARK 500 DA A 2 C5 - C6 - N6 ANGL. DEV. = 5.4 DEGREES REMARK 500 DA A 2 C3' - O3' - P ANGL. DEV. = 13.8 DEGREES REMARK 500 DG A 3 C3' - C2' - C1' ANGL. DEV. = 9.2 DEGREES REMARK 500 DG A 3 O4' - C1' - C2' ANGL. DEV. = -10.2 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = 11.9 DEGREES REMARK 500 DG A 3 C5 - N7 - C8 ANGL. DEV. = -3.1 DEGREES REMARK 500 DG A 3 N7 - C8 - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 DG A 3 C8 - N9 - C4 ANGL. DEV. = -5.9 DEGREES REMARK 500 DG A 3 C8 - N9 - C1' ANGL. DEV. = 8.1 DEGREES REMARK 500 DG A 3 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 DG A 4 O4' - C1' - C2' ANGL. DEV. = 3.1 DEGREES REMARK 500 DG A 4 N9 - C1' - C2' ANGL. DEV. = -15.1 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG A 4 C2 - N3 - C4 ANGL. DEV. = -3.9 DEGREES REMARK 500 DG A 4 C4 - C5 - N7 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG A 4 C5 - N7 - C8 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG A 4 N7 - C8 - N9 ANGL. DEV. = -5.7 DEGREES REMARK 500 DG A 4 C8 - N9 - C4 ANGL. DEV. = 5.5 DEGREES REMARK 500 DG A 4 N9 - C4 - C5 ANGL. DEV. = -6.6 DEGREES REMARK 500 DG A 4 N3 - C4 - N9 ANGL. DEV. = 7.1 DEGREES REMARK 500 DC A 5 O4' - C4' - C3' ANGL. DEV. = -3.5 DEGREES REMARK 500 DC A 5 O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 11.5 DEGREES REMARK 500 DC A 6 C1' - O4' - C4' ANGL. DEV. = 5.6 DEGREES REMARK 500 DC A 6 O4' - C1' - C2' ANGL. DEV. = -10.4 DEGREES REMARK 500 DC A 6 O4' - C1' - N1 ANGL. DEV. = 9.6 DEGREES REMARK 500 DC A 6 N3 - C4 - N4 ANGL. DEV. = 6.7 DEGREES REMARK 500 DC A 6 C5 - C4 - N4 ANGL. DEV. = -5.5 DEGREES REMARK 500 DT A 7 C1' - O4' - C4' ANGL. DEV. = 7.6 DEGREES REMARK 500 DT A 7 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 DT A 7 O4' - C1' - N1 ANGL. DEV. = 9.7 DEGREES REMARK 500 DT A 7 N3 - C4 - O4 ANGL. DEV. = -5.0 DEGREES REMARK 500 DT A 7 C5 - C4 - O4 ANGL. DEV. = 5.7 DEGREES REMARK 500 DT A 7 C4 - C5 - C7 ANGL. DEV. = 6.2 DEGREES REMARK 500 DT A 7 C6 - C5 - C7 ANGL. DEV. = -5.6 DEGREES REMARK 500 DT A 8 C5' - C4' - C3' ANGL. DEV. = 8.2 DEGREES REMARK 500 DT A 8 O4' - C1' - N1 ANGL. DEV. = 21.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 105 ANGLE DEVIATIONS. 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 DA A 1 0.10 SIDE CHAIN REMARK 500 DC A 5 0.07 SIDE CHAIN REMARK 500 DC A 6 0.09 SIDE CHAIN REMARK 500 DA B 11 0.10 SIDE CHAIN REMARK 500 DC B 15 0.07 SIDE CHAIN REMARK 500 DC B 16 0.09 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 B 1 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CPH A 33 O1 REMARK 620 2 CPH A 33 O9 76.7 REMARK 620 3 CPH B 23 O1 108.8 105.3 REMARK 620 4 CPH B 23 O9 109.5 170.1 80.4 REMARK 620 N 1 2 3 DBREF 1D83 A 1 8 PDB 1D83 1D83 1 8 DBREF 1D83 B 11 18 PDB 1D83 1D83 11 18 SEQRES 1 A 8 DA DA DG DG DC DC DT DT SEQRES 1 B 8 DA DA DG DG DC DC DT DT HET CDR C 1 19 HET CDR C 2 19 HET ERI C 3 29 HET ARI D 1 24 HET 1GL D 2 24 HET ARI E 1 24 HET 1GL E 2 24 HET CDR F 1 19 HET CDR F 2 19 HET ERI F 3 29 HET CPH A 33 49 HET MG B 1 1 HET CPH B 23 49 HETNAM CDR (2R,5S,6R)-6-METHYLTETRAHYDRO-2H-PYRAN-2,5-DIOL HETNAM ERI 3-C-METHYL-4-O-ACETYL-ALPHA-L-OLIVOPYRANOSE HETNAM ARI (2R,3R,6R)-6-HYDROXY-2-METHYLTETRAHYDRO-2H-PYRAN-3-YL HETNAM 2 ARI ACETATE HETNAM 1GL 2,6-DIDEOXY-4-O-METHYL-ALPHA-D-GALACTOPYRANOSE HETNAM CPH (1S)-5-DEOXY-1-O-METHYL-1-C-[(2R,3S)-3,5,7,10- HETNAM 2 CPH TETRAHYDROXY-6-METHYL-4-OXO-1,2,3,4- HETNAM 3 CPH TETRAHYDROANTHRACEN-2-YL]-D-XYLULOSE HETNAM MG MAGNESIUM ION HETSYN CDR 2,3-DIDEOXYFUCOSE HETSYN ERI 4-O-ACETYL-2,6-DIDEOXY-3-C-METHYL-BETA-L-ARABINO- HETSYN 2 ERI HEXOPYRANOSE; 3-C-METHYL-4-O-ACETYL-ALPHA-L-OLIVOSE; HETSYN 3 ERI 3-C-METHYL-4-O-ACETYL-L-OLIVOSE; 3-C-METHYL-4-O- HETSYN 4 ERI ACETYL-OLIVOSE HETSYN ARI [O4]-ACETOXY-2,3-DIDEOXYFUCOSE HETSYN 1GL 4-O-METHYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE; 2- HETSYN 2 1GL DEOXY-4-O-METHYL-ALPHA-D-FUCOPYRANOSE; 2,6-DIDEOXY-4- HETSYN 3 1GL O-METHYL-ALPHA-D-GALACTOSE; 2,6-DIDEOXY-4-O-METHYL-D- HETSYN 4 1GL GALACTOSE; 2,6-DIDEOXY-4-O-METHYL-GALACTOSE HETSYN CPH NONE FORMUL 3 CDR 4(C6 H12 O3) FORMUL 3 ERI 2(C9 H16 O5) FORMUL 4 ARI 2(C8 H14 O4) FORMUL 4 1GL 2(C7 H14 O4) FORMUL 7 CPH 2(C21 H24 O9) FORMUL 8 MG MG 2+ LINK C6 CPH A 33 O1 ARI D 1 1555 1555 1.39 LINK C2 CPH A 33 O1 CDR F 1 1555 1555 1.43 LINK C2 CPH B 23 O1 CDR C 1 1555 1555 1.43 LINK C6 CPH B 23 O1 ARI E 1 1555 1555 1.39 LINK C3 CDR C 1 O1 CDR C 2 1555 1555 1.45 LINK C3 CDR C 2 O1 ERI C 3 1555 1555 1.44 LINK C3 ARI D 1 O1 1GL D 2 1555 1555 1.45 LINK C3 ARI E 1 O1 1GL E 2 1555 1555 1.45 LINK C3 CDR F 1 O1 CDR F 2 1555 1555 1.45 LINK C3 CDR F 2 O1 ERI F 3 1555 1555 1.44 LINK O1 CPH A 33 MG MG B 1 1555 1555 1.89 LINK O9 CPH A 33 MG MG B 1 1555 1555 2.07 LINK MG MG B 1 O1 CPH B 23 1555 1555 1.89 LINK MG MG B 1 O9 CPH B 23 1555 1555 1.95 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