HEADER DNA 17-MAY-99 1QDA TITLE CRYSTAL STRUCTURE OF EPIDOXORUBICIN-FORMALDEHYDE VIRTUAL CROSSLINK OF TITLE 2 DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5' -D(CP*GP*CP*(G49)P*CP*GP)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: DOXORUBICIN COVALENTLY ATTACHED TO N2(G4) VIA COMPND 6 METHYLENE BRIDGE SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DOUBLE HELIX, DRUG-DNA COMPLEX, DNA EXPDTA X-RAY DIFFRACTION AUTHOR E.R.PODELL,D.J.HARRINGTON,D.J.TAATJES,T.H.KOCH REVDAT 6 14-FEB-24 1QDA 1 REMARK LINK REVDAT 5 04-APR-18 1QDA 1 REMARK REVDAT 4 04-OCT-17 1QDA 1 REMARK REVDAT 3 12-MAR-14 1QDA 1 JRNL VERSN REVDAT 2 24-FEB-09 1QDA 1 VERSN REVDAT 1 15-SEP-99 1QDA 0 JRNL AUTH E.R.PODELL,D.J.HARRINGTON,D.J.TAATJES,T.H.KOCH JRNL TITL CRYSTAL STRUCTURE OF EPIDOXORUBICIN-FORMALDEHYDE VIRTUAL JRNL TITL 2 CROSSLINK OF DNA AND EVIDENCE FOR ITS FORMATION IN HUMAN JRNL TITL 3 BREAST-CANCER CELLS. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 55 1516 1999 JRNL REFN ISSN 0907-4449 JRNL PMID 10489446 JRNL DOI 10.1107/S0907444999008161 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.J.TAATJES,D.J.FENICK,G.GAUDIANO,T.H.KOCH REMARK 1 TITL A REDOX PATHWAY LEADING TO THE ALKYLATION OF NUCLEIC ACIDS REMARK 1 TITL 2 BY DOXORUBICIN AND RELATED ANTHRACYCLINES: APPLICATION TO REMARK 1 TITL 3 THE DESIGN OF ANTITUMOR DRUGS FOR RESISTANT CANCER. REMARK 1 REF CURR.PHARM.DES. V. 4 203 1998 REMARK 1 REFN ISSN 1381-6128 REMARK 1 PMID 10197040 REMARK 1 REFERENCE 2 REMARK 1 AUTH D.J.TAATJES,D.J.FENICK,T.H.KOCH REMARK 1 TITL EPIDOXOFORM: A HYDROLYTICALLY MORE STABLE REMARK 1 TITL 2 ANTHRACYCLINE-FORMALDEHYDE CONJUGATE TOXIC TO RESISTANT REMARK 1 TITL 3 TUMOR CELLS REMARK 1 REF J.MED.CHEM. V. 41 2452 1998 REMARK 1 REFN ISSN 0022-2623 REMARK 1 DOI 10.1021/JM970739S REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : G. PARKINSON, J. VOJTECHOVSKY, L. CLOWNEY, REMARK 3 A.T. BRUNGER, H.M. BERMAN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 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) (%) : 84.5 REMARK 3 NUMBER OF REFLECTIONS : 2612 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 17.300 REMARK 3 FREE R VALUE TEST SET COUNT : 529 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 : 121 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 30 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : 0.020 REMARK 3 BOND ANGLES (DEGREES) : 2.100 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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: USED ALL THE REFLECTIONS IN THE FINAL REMARK 3 SERIES OF REFINEMENT CYCLES REMARK 4 REMARK 4 1QDA 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_1000009101. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JAN-98 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 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) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3101 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 12.00 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.7 REMARK 200 DATA REDUNDANCY IN SHELL : 9.50 REMARK 200 R MERGE FOR SHELL (I) : 0.30900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, FORMALDEHYDE, CACODYLATE, REMARK 280 SPERMINE, BARIUM CHLORIDE, PH 6.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.27000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 14.05500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 14.05500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 13.13500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 14.05500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 14.05500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.40500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 14.05500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 14.05500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 13.13500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 14.05500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 14.05500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 39.40500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 26.27000 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 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 350 BIOMT1 2 0.000000 -1.000000 0.000000 28.11000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 28.11000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 26.27000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O HOH A 105 O HOH A 121 1.97 REMARK 500 OP1 DG A 6 O HOH A 123 2.08 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 DC A 5 N1 DC A 5 C2 -0.064 REMARK 500 DG A 6 O3' DG A 6 C3' -0.042 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 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.0 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 DC A 5 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DM6 A 100 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1D33 RELATED DB: PDB REMARK 900 1D33 CONTAINS THE SAME DNA COMPLEXED WITH DAUNOMYCIN REMARK 900 RELATED ID: 1D15 RELATED DB: PDB REMARK 900 1D15 CONTAINS THE SAME DRUG COMPLEXED WITH D(CGATCG) REMARK 900 RELATED ID: 1D54 RELATED DB: PDB REMARK 900 1D54 CONTAINS THE SAME DRUG COMPLEXED WITH D(TGTACA) DBREF 1QDA A 1 6 PDB 1QDA 1QDA 1 6 SEQRES 1 A 6 DC DG DC G49 DC DG MODRES 1QDA G49 A 4 DG HET G49 A 4 23 HET DM6 A 100 39 HETNAM G49 N2-METHYL-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM DM6 4'-EPIDOXORUBICIN HETSYN DM6 4'-EPIADRIAMYCIN FORMUL 1 G49 C11 H16 N5 O7 P FORMUL 2 DM6 C27 H30 N O11 1+ FORMUL 3 HOH *30(H2 O) LINK O3' DC A 3 P G49 A 4 1555 1555 1.58 LINK O3' G49 A 4 P DC A 5 1555 1555 1.61 LINK CM2 G49 A 4 N3' DM6 A 100 1555 1555 1.52 SITE 1 AC1 10 DC A 1 DG A 2 DC A 3 G49 A 4 SITE 2 AC1 10 DC A 5 DG A 6 HOH A 101 HOH A 106 SITE 3 AC1 10 HOH A 124 HOH A 125 CRYST1 28.110 28.110 52.540 90.00 90.00 90.00 P 41 21 2 8 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 0.035575 0.000000 0.000000 0.00000 SCALE2 0.000000 0.035575 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019033 0.00000