HEADER DNA 01-OCT-01 1K2Z TITLE THE CRYSTAL STRUCTURE OF D(GGCCAATTGG) COMPLEXED WITH DISTAMYCIN. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE IS SYNTHESIZED BY OSWELL DNA SERVICE SOURCE 4 (SOUTHAMPTON, UK). KEYWDS B-DNA DOUBLE HELIX, BASE TRIPLETS, MINOR GROOVE BINDING, DRUG, KEYWDS 2 DISTAMYCIN, DNA EXPDTA X-RAY DIFFRACTION AUTHOR K.UYTTERHOEVEN,L.VAN MEERVELT REVDAT 4 03-APR-24 1K2Z 1 REMARK REVDAT 3 07-FEB-24 1K2Z 1 REMARK REVDAT 2 24-FEB-09 1K2Z 1 VERSN REVDAT 1 09-AUG-02 1K2Z 0 JRNL AUTH K.UYTTERHOEVEN,J.SPONER,L.VAN MEERVELT JRNL TITL TWO 1 : 1 BINDING MODES FOR DISTAMYCIN IN THE MINOR GROOVE JRNL TITL 2 OF D(GGCCAATTGG). JRNL REF EUR.J.BIOCHEM. V. 269 2868 2002 JRNL REFN ISSN 0014-2956 JRNL PMID 12071949 JRNL DOI 10.1046/J.1432-1033.2002.02952.X REMARK 2 REMARK 2 RESOLUTION. 2.38 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) : 2.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.8 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) : 0.214 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.214 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) : 2299 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.203 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.203 REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 83.800 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 1928 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 410 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 46 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.020 REMARK 3 ANGLE DISTANCES (A) : 0.050 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: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : USER DEFINED REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1K2Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-OCT-01. REMARK 100 THE DEPOSITION ID IS D_1000014495. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-APR-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9116 REMARK 200 MONOCHROMATOR : SI 111 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 : 2351 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.380 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.25100 REMARK 200 FOR SHELL : 5.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NDB ENTRY DD0002 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, MAGNESIUM CHLORIDE, CACODYLATE, REMARK 280 SPERMINE, PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 13.05300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.56900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.46400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.56900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.05300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.46400 REMARK 290 SMTRY3 4 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 3 C1' DC A 3 N1 0.084 REMARK 500 DC A 4 C1' DC A 4 N1 0.080 REMARK 500 DA A 5 C1' DA A 5 N9 -0.097 REMARK 500 DA A 6 C1' DA A 6 N9 -0.100 REMARK 500 DC B 13 C1' DC B 13 N1 0.080 REMARK 500 DC B 14 C1' DC B 14 N1 0.079 REMARK 500 DA B 15 C1' DA B 15 N9 -0.097 REMARK 500 DA B 16 C1' DA B 16 N9 -0.094 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 1 N9 - C1' - C2' ANGL. DEV. = 10.0 DEGREES REMARK 500 DG A 1 O4' - C1' - N9 ANGL. DEV. = -13.5 DEGREES REMARK 500 DG A 2 N9 - C1' - C2' ANGL. DEV. = 14.4 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = -12.8 DEGREES REMARK 500 DC A 3 O4' - C4' - C3' ANGL. DEV. = 4.5 DEGREES REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = -5.1 DEGREES REMARK 500 DC A 3 C6 - N1 - C1' ANGL. DEV. = 8.2 DEGREES REMARK 500 DC A 3 C2 - N1 - C1' ANGL. DEV. = -10.3 DEGREES REMARK 500 DC A 4 C6 - N1 - C1' ANGL. DEV. = 11.2 DEGREES REMARK 500 DC A 4 C2 - N1 - C1' ANGL. DEV. = -10.9 DEGREES REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = -6.9 DEGREES REMARK 500 DA A 6 O4' - C1' - N9 ANGL. DEV. = -8.1 DEGREES REMARK 500 DT A 7 N1 - C1' - C2' ANGL. DEV. = 12.3 DEGREES REMARK 500 DT A 7 O4' - C1' - N1 ANGL. DEV. = -11.1 DEGREES REMARK 500 DT A 7 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 DT A 8 N1 - C1' - C2' ANGL. DEV. = 11.0 DEGREES REMARK 500 DT A 8 O4' - C1' - N1 ANGL. DEV. = -9.4 DEGREES REMARK 500 DG A 9 N9 - C1' - C2' ANGL. DEV. = 8.8 DEGREES REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = -13.1 DEGREES REMARK 500 DG A 10 N9 - C1' - C2' ANGL. DEV. = 10.2 DEGREES REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = -11.8 DEGREES REMARK 500 DG B 11 N9 - C1' - C2' ANGL. DEV. = 9.2 DEGREES REMARK 500 DG B 11 O4' - C1' - N9 ANGL. DEV. = -12.3 DEGREES REMARK 500 DG B 12 N9 - C1' - C2' ANGL. DEV. = 11.3 DEGREES REMARK 500 DG B 12 O4' - C1' - N9 ANGL. DEV. = -14.9 DEGREES REMARK 500 DC B 13 C6 - N1 - C1' ANGL. DEV. = 11.4 DEGREES REMARK 500 DC B 13 C2 - N1 - C1' ANGL. DEV. = -11.4 DEGREES REMARK 500 DC B 14 C6 - N1 - C1' ANGL. DEV. = 10.0 DEGREES REMARK 500 DC B 14 C2 - N1 - C1' ANGL. DEV. = -10.2 DEGREES REMARK 500 DA B 15 O4' - C1' - N9 ANGL. DEV. = -7.6 DEGREES REMARK 500 DA B 16 O4' - C1' - N9 ANGL. DEV. = -7.9 DEGREES REMARK 500 DT B 17 N1 - C1' - C2' ANGL. DEV. = 12.3 DEGREES REMARK 500 DT B 17 O4' - C1' - N1 ANGL. DEV. = -9.4 DEGREES REMARK 500 DT B 18 N1 - C1' - C2' ANGL. DEV. = 11.9 DEGREES REMARK 500 DT B 18 O4' - C1' - N1 ANGL. DEV. = -8.0 DEGREES REMARK 500 DG B 19 N9 - C1' - C2' ANGL. DEV. = 10.2 DEGREES REMARK 500 DG B 19 O4' - C1' - N9 ANGL. DEV. = -13.1 DEGREES REMARK 500 DG B 20 N9 - C1' - C2' ANGL. DEV. = 9.3 DEGREES REMARK 500 DG B 20 O4' - C1' - N9 ANGL. DEV. = -11.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: DD0042 RELATED DB: NDB REMARK 900 DD0042 IS THE CRYSTAL STRUCTURE OF D(GGCCAATTGG) COMPLEXED WITH REMARK 900 DISTAMYCIN. REMARK 900 RELATED ID: BD0006 RELATED DB: NDB REMARK 900 BD0006 IS B-DNA AT ATOMIC RESOLUTION REVEALS EXTENDED HYDRATION REMARK 900 PATTERNS. REMARK 900 RELATED ID: DD0002 RELATED DB: NDB REMARK 900 DD0002 IS THE CRYSTAL STRUCTURE OF D(GGCCAATTGG) COMPLEXED WITH REMARK 900 DAPI REVEALS NOVEL BINDING MODE. REMARK 900 RELATED ID: UDJ049 RELATED DB: NDB REMARK 900 UDJ049 IS PARALLEL AND ANTIPARALLEL (G.GC)2 TRIPLE HELIX FRAGMENTS REMARK 900 IN A CRYSTAL STRUCTURE. DBREF 1K2Z A 1 10 PDB 1K2Z 1K2Z 1 10 DBREF 1K2Z B 11 20 PDB 1K2Z 1K2Z 11 20 SEQRES 1 A 10 DG DG DC DC DA DA DT DT DG DG SEQRES 1 B 10 DG DG DC DC DA DA DT DT DG DG HET DMY A 21 35 HETNAM DMY DISTAMYCIN A HETSYN DMY DISTAMYCIN; STALLIMYCIN FORMUL 3 DMY C22 H27 N9 O4 FORMUL 4 HOH *46(H2 O) SITE 1 AC1 12 DA A 5 DA A 6 DT A 7 DT A 8 SITE 2 AC1 12 DG A 9 HOH A 39 DA B 15 DA B 16 SITE 3 AC1 12 DT B 17 DT B 18 DG B 19 HOH B 65 CRYST1 26.106 40.928 53.138 90.00 90.00 90.00 P 21 21 21 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 0.038305 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024433 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018819 0.00000