PDB Short entry for 360D HEADER DNA 29-OCT-97 360D TITLE STRUCTURE OF 2,5-BIS{[4-(N-ETHYLAMIDINO)PHENYL]}FURAN COMPLEXED TO 5'- TITLE 2 D(CPGPCPGPAPAPTPTPCPGPCPG)-3'. A MINOR GROOVE DRUG COMPLEX, SHOWING TITLE 3 PATTERNS OF GROOVE HYDRATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*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 B-DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, DNA EXPDTA X-RAY DIFFRACTION AUTHOR A.GUERRI,I.J.SIMPSON,S.NEIDLE REVDAT 8 02-AUG-23 360D 1 REMARK LINK REVDAT 7 08-APR-20 360D 1 AUTHOR REVDAT 6 07-MAR-18 360D 1 REMARK REVDAT 5 26-APR-17 360D 1 SOURCE AUTHOR REVDAT 4 25-APR-12 360D 1 FORMUL HETNAM VERSN REVDAT 3 24-FEB-09 360D 1 VERSN REVDAT 2 01-APR-03 360D 1 JRNL REVDAT 1 16-JUL-98 360D 0 JRNL AUTH A.GUERRI,I.J.SIMPSON,S.NEIDLE JRNL TITL VISUALISATION OF EXTENSIVE WATER RIBBONS AND NETWORKS IN A JRNL TITL 2 DNA MINOR-GROOVE DRUG COMPLEX. JRNL REF NUCLEIC ACIDS RES. V. 26 2873 1998 JRNL REFN ISSN 0305-1048 JRNL PMID 9611230 JRNL DOI 10.1093/NAR/26.12.2873 REMARK 2 REMARK 2 RESOLUTION. 1.85 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.4 REMARK 3 CROSS-VALIDATION METHOD : NONE 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) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.170 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) : 5634 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.166 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)) : 5386 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 : 28 REMARK 3 SOLVENT ATOMS : 219 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 733.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 260.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 2904 REMARK 3 NUMBER OF RESTRAINTS : 3734 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)201-22 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : PARKINSON ET AL. REMARK 3 SPECIAL CASE: STEREOCHEMISTRY OF LIGAND FROM MM CALCULATIONS REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 360D 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_1000178830. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-97 REMARK 200 TEMPERATURE (KELVIN) : 100.00 REMARK 200 PH : 7.00 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5634 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 7.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.02200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 33.1800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.7 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 : 14.67 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NDB ENTRY GDL045 (PDB: 289D) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.00, VAPOR DIFFUSION, TEMPERATURE REMARK 280 288.0K 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 12.21001 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.94025 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.96965 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.94025 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.21001 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.96965 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 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 N1 - C1' - C2' ANGL. DEV. = 8.8 DEGREES REMARK 500 DC A 1 O4' - C1' - N1 ANGL. DEV. = -11.2 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = -6.2 DEGREES REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = -7.0 DEGREES REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = -6.6 DEGREES REMARK 500 DA A 6 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 DT A 7 O4' - C1' - N1 ANGL. DEV. = -5.3 DEGREES REMARK 500 DT A 8 O4' - C1' - N1 ANGL. DEV. = -6.0 DEGREES REMARK 500 DC A 9 N1 - C1' - C2' ANGL. DEV. = 8.9 DEGREES REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = -12.6 DEGREES REMARK 500 DC A 9 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG A 10 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = -10.3 DEGREES REMARK 500 DG A 12 O4' - C1' - N9 ANGL. DEV. = -4.8 DEGREES REMARK 500 DC B 13 O5' - C5' - C4' ANGL. DEV. = -16.1 DEGREES REMARK 500 DG B 14 O4' - C1' - N9 ANGL. DEV. = -4.3 DEGREES REMARK 500 DC B 15 O4' - C1' - N1 ANGL. DEV. = -10.3 DEGREES REMARK 500 DG B 16 N1 - C6 - O6 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG B 16 C5 - C6 - O6 ANGL. DEV. = 4.2 DEGREES REMARK 500 DA B 17 O4' - C1' - N9 ANGL. DEV. = -5.7 DEGREES REMARK 500 DA B 18 O4' - C1' - N9 ANGL. DEV. = -5.1 DEGREES REMARK 500 DT B 19 N1 - C1' - C2' ANGL. DEV. = 8.4 DEGREES REMARK 500 DT B 19 O4' - C1' - N1 ANGL. DEV. = -6.9 DEGREES REMARK 500 DT B 20 N1 - C1' - C2' ANGL. DEV. = 8.4 DEGREES REMARK 500 DT B 20 O4' - C1' - N1 ANGL. DEV. = -7.1 DEGREES REMARK 500 DC B 21 O4' - C1' - N1 ANGL. DEV. = -11.6 DEGREES REMARK 500 DC B 23 O4' - C1' - N1 ANGL. DEV. = -7.3 DEGREES 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 26 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 240 O REMARK 620 2 HOH A 241 O 90.1 REMARK 620 3 HOH A 242 O 171.3 82.3 REMARK 620 4 HOH A 243 O 94.1 172.5 93.9 REMARK 620 5 HOH A 244 O 92.5 81.7 90.6 91.9 REMARK 620 6 HOH A 245 O 79.9 88.0 95.6 98.9 167.2 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 MG A 26 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BPF B 25 DBREF 360D A 1 12 PDB 360D 360D 1 12 DBREF 360D B 13 24 PDB 360D 360D 13 24 SEQRES 1 A 12 DC DG DC DG DA DA DT DT DC DG DC DG SEQRES 1 B 12 DC DG DC DG DA DA DT DT DC DG DC DG HET MG A 26 1 HET BPF B 25 27 HETNAM MG MAGNESIUM ION HETNAM BPF N,N'-(FURAN-2,5-DIYLBIS{BENZENE-4,1-DIYL[(Z)- HETNAM 2 BPF AMINOMETHYLYLIDENE]})DIETHANAMINIUM HETSYN BPF DB185; FURAMIDINE DERIVATIVE FORMUL 3 MG MG 2+ FORMUL 4 BPF C22 H26 N4 O 2+ FORMUL 5 HOH *219(H2 O) LINK MG MG A 26 O HOH A 240 1555 1555 2.30 LINK MG MG A 26 O HOH A 241 1555 1555 1.94 LINK MG MG A 26 O HOH A 242 1555 1555 2.08 LINK MG MG A 26 O HOH A 243 1555 1555 1.89 LINK MG MG A 26 O HOH A 244 1555 1555 2.18 LINK MG MG A 26 O HOH A 245 1555 1555 2.23 SITE 1 AC1 6 HOH A 240 HOH A 241 HOH A 242 HOH A 243 SITE 2 AC1 6 HOH A 244 HOH A 245 SITE 1 AC2 12 DA A 6 DT A 7 DT A 8 DC A 9 SITE 2 AC2 12 HOH A 197 DA B 18 DT B 19 DT B 20 SITE 3 AC2 12 DC B 21 HOH B 45 HOH B 72 HOH B 201 CRYST1 24.240 39.940 65.880 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 0.040950 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025038 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015179 0.00000