HEADER DNA 15-JAN-97 308D TITLE BINDING OF DAUNOMYCIN TO B-D-GLUCOSYLATED DNA FOUND IN PROTOZOA TITLE 2 TRYPANOSOMA BRUCEI STUDIED BY X-RAY CRYSTALLOGRAPH COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*TP*AP*CP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS RIGHT HANDED DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, MODIFIED, DNA EXPDTA X-RAY DIFFRACTION AUTHOR Y.-G.GAO,H.ROBINSON,E.R.WIJSMAN,G.A.VAN DER MAREL,J.H.VAN BOOM,A.H.- AUTHOR 2 J.WANG REVDAT 5 03-APR-24 308D 1 REMARK REVDAT 4 21-FEB-24 308D 1 HETSYN REVDAT 3 29-JUL-20 308D 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 24-FEB-09 308D 1 VERSN REVDAT 1 21-JAN-97 308D 0 JRNL AUTH Y.-G.GAO,H.ROBINSON,E.R.WIJSMAN,G.A.VAN DER MAREL, JRNL AUTH 2 J.H.VAN BOOM,A.H.-J.WANG JRNL TITL BINDING OF DAUNOMYCIN TO BETA-D-GLUCOSYLATED DNA FOUND IN JRNL TITL 2 PROTOZOA TRYPANOSOMA BRUCEI STUDIED BY X-RAY CRYSTALLOGRAPHY JRNL REF J.AM.CHEM.SOC. V. 119 1496 1997 JRNL REFN ISSN 0002-7863 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 4678 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 240 REMARK 3 HETEROGEN ATOMS : 103 REMARK 3 SOLVENT ATOMS : 105 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.019 REMARK 3 BOND ANGLES (DEGREES) : 3.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 308D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000178776. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-AUG-96 REMARK 200 TEMPERATURE (KELVIN) : 293.00 REMARK 200 PH : 6.00 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4688 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: ULTIMA REMARK 200 STARTING MODEL: DDF001 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.00, VAPOR DIFFUSION, TEMPERATURE REMARK 280 293.00K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 DC A 1 C5' DC A 1 C4' 0.057 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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG A 2 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 DC A 5 O4' - C4' - C3' ANGL. DEV. = 3.6 DEGREES REMARK 500 DC A 5 C1' - O4' - C4' ANGL. DEV. = -7.3 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC B 7 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG B 8 C1' - O4' - C4' ANGL. DEV. = -7.2 DEGREES REMARK 500 DG B 8 O4' - C1' - N9 ANGL. DEV. = 2.2 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 DC A 5 0.07 SIDE CHAIN REMARK 500 DC B 11 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 A 16 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT A 3 OP1 REMARK 620 2 HOH A 113 O 91.8 REMARK 620 3 HOH A 114 O 98.3 169.8 REMARK 620 4 HOH A 115 O 89.8 88.3 90.1 REMARK 620 5 HOH A 116 O 175.2 83.5 86.4 89.0 REMARK 620 6 HOH A 117 O 95.1 92.3 88.4 175.1 86.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 17 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA A 4 OP2 REMARK 620 2 HOH A 118 O 98.4 REMARK 620 3 HOH A 119 O 90.9 170.1 REMARK 620 4 HOH A 120 O 96.8 86.6 89.0 REMARK 620 5 HOH A 121 O 174.8 85.9 85.0 86.3 REMARK 620 6 HOH A 122 O 90.3 90.5 92.9 172.7 86.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 15 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 107 O REMARK 620 2 HOH A 108 O 176.6 REMARK 620 3 HOH B 109 O 89.9 90.5 REMARK 620 4 HOH B 110 O 87.3 89.4 91.4 REMARK 620 5 HOH B 111 O 91.4 88.4 176.9 91.5 REMARK 620 6 HOH B 112 O 88.6 94.8 89.7 175.7 87.5 REMARK 620 N 1 2 3 4 5 DBREF 308D A 1 6 PDB 308D 308D 1 6 DBREF 308D B 7 12 PDB 308D 308D 7 12 SEQRES 1 A 6 DC DG DT DA DC DG SEQRES 1 B 6 DC DG DT DA DC DG HET BGC A 7 12 HET DM1 A 14 38 HET MG A 16 1 HET MG A 17 1 HET BGC B 13 12 HET DM1 B 14 38 HET MG B 15 1 HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM DM1 DAUNOMYCIN HETNAM MG MAGNESIUM ION HETSYN BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN DM1 DAUNORUBICIN FORMUL 3 BGC 2(C6 H12 O6) FORMUL 4 DM1 2(C27 H29 N O10) FORMUL 5 MG 3(MG 2+) FORMUL 10 HOH *105(H2 O) LINK C7 DT A 3 O1 BGC A 7 1555 1555 1.41 LINK C7 DT B 9 O1 BGC B 13 1555 1555 1.40 LINK OP1 DT A 3 MG MG A 16 1555 1555 2.20 LINK OP2 DA A 4 MG MG A 17 1555 1555 2.24 LINK MG MG A 16 O HOH A 113 1555 1555 1.95 LINK MG MG A 16 O HOH A 114 1555 1555 1.95 LINK MG MG A 16 O HOH A 115 1555 1555 1.94 LINK MG MG A 16 O HOH A 116 1555 1555 1.89 LINK MG MG A 16 O HOH A 117 1555 1555 1.93 LINK MG MG A 17 O HOH A 118 1555 1555 1.95 LINK MG MG A 17 O HOH A 119 1555 1555 1.94 LINK MG MG A 17 O HOH A 120 1555 1555 1.93 LINK MG MG A 17 O HOH A 121 1555 1555 1.94 LINK MG MG A 17 O HOH A 122 1555 1555 1.95 LINK O HOH A 107 MG MG B 15 1555 1555 1.92 LINK O HOH A 108 MG MG B 15 1555 1555 1.95 LINK MG MG B 15 O HOH B 109 1555 1555 1.93 LINK MG MG B 15 O HOH B 110 1555 1555 1.91 LINK MG MG B 15 O HOH B 111 1555 1555 1.89 LINK MG MG B 15 O HOH B 112 1555 1555 1.95 CRYST1 18.619 20.096 26.553 69.09 90.40 108.03 P 1 2 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 0.053709 0.017482 -0.006625 0.00000 SCALE2 0.000000 0.052331 -0.021042 0.00000 SCALE3 0.000000 0.000000 0.040592 0.00000