HEADER DNA 21-SEP-98 427D TITLE 5'-D(*CP*GP*CP*(CH2-DM1)GP*CP*G)-3' COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*(G49)P*CP*G)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DEOXYRIBONUCLEIC ACID, DRUG COMPLEX, FORMALDEHYDE CROSS-LINK, ATOMIC KEYWDS 2 RESOLUTION, DOUBLE BACKBONE CONFORMATION, DNA EXPDTA X-RAY DIFFRACTION AUTHOR G.SCHUERMAN,L.VAN MEERVELT REVDAT 5 03-APR-24 427D 1 REMARK REVDAT 4 27-DEC-23 427D 1 REMARK LINK REVDAT 3 04-OCT-17 427D 1 REMARK REVDAT 2 24-FEB-09 427D 1 VERSN REVDAT 1 24-JAN-00 427D 0 JRNL AUTH G.SCHUERMAN,L.VAN MEERVELT JRNL TITL CONFORMATIONAL FLEXIBILITY OF THE DNA BACKBONE. JRNL REF J.AM.CHEM.SOC. V. 122 232 2000 JRNL REFN ISSN 0002-7863 JRNL DOI 10.1021/JA992180M REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.102 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.101 REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 8581 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.101 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 8277 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 : 38 REMARK 3 SOLVENT ATOMS : 65 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 97.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 222.47 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 27 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 2327 REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201- 228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC UNRESTRAINED REFIN. REMARK 4 REMARK 4 427D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-SEP-98. REMARK 100 THE DEPOSITION ID IS D_1000001333. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-97 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M 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 : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8581 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.2700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.09400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 10.58 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: DDF023 REMARK 200 REMARK 200 REMARK: DDF023 USED AS STARTING MODEL FOR REFINEMENT REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K 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 25.92900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 13.90900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 13.90900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 12.96450 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 13.90900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 13.90900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 38.89350 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 13.90900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 13.90900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 12.96450 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 13.90900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 13.90900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 38.89350 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 25.92900 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 27.81800 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 27.81800 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 25.92900 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 N1 DC A 1 C6 0.053 REMARK 500 DC A 1 C5 DC A 1 C6 -0.054 REMARK 500 DG A 2 C5' DG A 2 C4' 0.047 REMARK 500 DC A 3 C5' DC A 3 C4' 0.061 REMARK 500 DC A 3 C5' DC A 3 C4' 0.049 REMARK 500 DC A 3 C2' DC A 3 C1' 0.168 REMARK 500 DC A 3 C2' DC A 3 C1' -0.115 REMARK 500 DC A 3 O4' DC A 3 C1' -0.080 REMARK 500 DC A 5 C4 DC A 5 C5 -0.058 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 N3 - C4 - C5 ANGL. DEV. = -2.4 DEGREES REMARK 500 DC A 1 C4 - C5 - C6 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC A 1 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG A 2 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DC A 3 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DC A 3 C3' - C2' - C1' ANGL. DEV. = -5.1 DEGREES REMARK 500 DC A 3 O4' - C1' - C2' ANGL. DEV. = 3.6 DEGREES REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = -5.1 DEGREES REMARK 500 DC A 3 C6 - N1 - C2 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC A 3 C6 - N1 - C1' ANGL. DEV. = -7.2 DEGREES REMARK 500 DC A 3 C2 - N1 - C1' ANGL. DEV. = -10.2 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 3 0.10 SIDE CHAIN REMARK 500 DC A 5 0.10 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 DM1 A 7 DBREF 427D A 1 6 PDB 427D 427D 1 6 SEQRES 1 A 6 DC DG DC G49 DC DG MODRES 427D G49 A 4 DG HET G49 A 4 29 HET DM1 A 7 38 HETNAM G49 N2-METHYL-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM DM1 DAUNOMYCIN HETSYN DM1 DAUNORUBICIN FORMUL 1 G49 C11 H16 N5 O7 P FORMUL 2 DM1 C27 H29 N O10 FORMUL 3 HOH *65(H2 O) LINK O3'A DC A 3 P AG49 A 4 1555 1555 1.62 LINK O3'B DC A 3 P BG49 A 4 1555 1555 1.60 LINK O3'BG49 A 4 P B DC A 5 1555 1555 1.58 LINK O3'AG49 A 4 P A DC A 5 1555 1555 1.64 LINK CM2 G49 A 4 N3' DM1 A 7 1555 1555 1.57 SITE 1 AC1 14 DC A 1 DG A 2 DC A 3 G49 A 4 SITE 2 AC1 14 DC A 5 DG A 6 HOH A 8 HOH A 14 SITE 3 AC1 14 HOH A 15 HOH A 21 HOH A 22 HOH A 50 SITE 4 AC1 14 HOH A 64 HOH A 65 CRYST1 27.818 27.818 51.858 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 0.035948 0.000000 0.000000 0.00000 SCALE2 0.000000 0.035948 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019283 0.00000