HEADER DNA 20-AUG-15 5DAM TITLE CRYSTAL STRUCTURE OF P-IODOHOECHST BOUND TO D(CGCAAATTTGCG) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS MINOR GROOVE BINDER DNA, DNA EXPDTA X-RAY DIFFRACTION AUTHOR G.R.CLARK REVDAT 3 04-MAR-26 5DAM 1 REMARK REVDAT 2 06-MAR-24 5DAM 1 REMARK LINK REVDAT 1 16-MAR-16 5DAM 0 JRNL AUTH G.R.CLARK JRNL TITL CRYSTAL STRUCTURE OF P-IODOHOECHST BOUND TO D(CGCAAATTTGCG) JRNL REF INT J RADIAT BIOL. 2016 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.4 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.186 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.178 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 11.200 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 477 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 4270 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.172 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.165 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 11.200 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 418 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 3741 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 486 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 135 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 653.79 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 2619 REMARK 3 NUMBER OF RESTRAINTS : 2589 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 ANGLE DISTANCES (A) : 0.027 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.009 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.007 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.011 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.069 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5DAM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212759. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JAN-01 REMARK 200 TEMPERATURE (KELVIN) : 113 REMARK 200 PH : 7.0 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 RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54179 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : OSMIC OPTICS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4783 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 4.210 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : 0.04900 REMARK 200 FOR THE DATA SET : 22.1700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.22600 REMARK 200 R SYM FOR SHELL (I) : 0.22300 REMARK 200 FOR SHELL : 5.620 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NDB ID GDL039 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP, 19 DEG C, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 292K 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 12.31900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.17200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.20400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.17200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.31900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.20400 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL 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 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. = -7.4 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = -4.7 DEGREES REMARK 500 DG A 2 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 DT A 8 N3 - C2 - O2 ANGL. DEV. = -3.9 DEGREES REMARK 500 DT A 8 N3 - C4 - O4 ANGL. DEV. = -3.7 DEGREES REMARK 500 DC A 11 N1 - C1' - C2' ANGL. DEV. = 8.8 DEGREES REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = -7.3 DEGREES REMARK 500 DG A 12 O4' - C1' - N9 ANGL. DEV. = -6.0 DEGREES REMARK 500 DG A 12 C5 - C6 - O6 ANGL. DEV. = -3.6 DEGREES REMARK 500 DC B 3 O4' - C1' - N1 ANGL. DEV. = -6.2 DEGREES REMARK 500 DA B 5 O4' - C1' - N9 ANGL. DEV. = -4.2 DEGREES REMARK 500 DG B 10 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 375 DISTANCE = 5.95 ANGSTROMS 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 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 318 O REMARK 620 2 HOH A 325 O 91.5 REMARK 620 3 HOH A 329 O 89.1 90.8 REMARK 620 4 HOH A 340 O 89.7 178.1 90.6 REMARK 620 5 HOH A 347 O 178.5 89.9 90.5 88.9 REMARK 620 6 HOH B 105 O 89.7 89.5 178.7 89.1 90.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 58F A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 DBREF 5DAM A 1 12 PDB 5DAM 5DAM 1 12 DBREF 5DAM B 1 12 PDB 5DAM 5DAM 1 12 SEQRES 1 A 12 DC DG DC DA DA DA DT DT DT DG DC DG SEQRES 1 B 12 DC DG DC DA DA DA DT DT DT DG DC DG HET 58F A 201 32 HET MG A 202 1 HETNAM 58F P-IODO HOECHST HETNAM MG MAGNESIUM ION HETSYN 58F 2'-(4-IODOPHENYL)-6-(4-METHYLPIPERAZIN-1-YL)-1H,3'H-2, HETSYN 2 58F 5'-BIBENZIMIDAZOLE FORMUL 3 58F C25 H23 I N6 FORMUL 4 MG MG 2+ FORMUL 5 HOH *135(H2 O) LINK MG MG A 202 O HOH A 318 1555 1555 2.11 LINK MG MG A 202 O HOH A 325 1555 1555 2.13 LINK MG MG A 202 O HOH A 329 1555 3657 2.12 LINK MG MG A 202 O HOH A 340 1555 3657 2.13 LINK MG MG A 202 O HOH A 347 1555 3657 2.12 LINK MG MG A 202 O HOH B 105 1555 1555 2.13 SITE 1 AC1 12 DT A 7 DT A 8 DT A 9 DG A 10 SITE 2 AC1 12 DC A 11 HOH A 312 HOH A 314 DA B 5 SITE 3 AC1 12 DA B 6 DT B 7 DT B 8 DG B 12 SITE 1 AC2 6 HOH A 318 HOH A 325 HOH A 329 HOH A 340 SITE 2 AC2 6 HOH A 347 HOH B 105 CRYST1 24.638 40.408 64.344 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 0.040588 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024748 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015541 0.00000 CONECT 489 491 493 520 CONECT 490 492 494 495 CONECT 491 489 492 CONECT 492 490 491 CONECT 493 489 494 CONECT 494 490 493 CONECT 495 490 502 503 CONECT 496 497 501 502 CONECT 497 496 498 503 CONECT 498 497 499 CONECT 499 498 500 CONECT 500 499 501 504 CONECT 501 496 500 CONECT 502 495 496 CONECT 503 495 497 CONECT 504 500 510 511 CONECT 505 506 510 512 CONECT 506 505 507 511 CONECT 507 506 508 CONECT 508 507 509 CONECT 509 508 512 513 CONECT 510 504 505 CONECT 511 504 506 CONECT 512 505 509 CONECT 513 509 515 518 CONECT 514 516 517 519 CONECT 515 513 516 CONECT 516 514 515 CONECT 517 514 518 CONECT 518 513 517 CONECT 519 514 CONECT 520 489 CONECT 521 539 546 601 CONECT 539 521 CONECT 546 521 CONECT 601 521 MASTER 247 0 2 0 0 0 5 6 654 2 36 2 END