HEADER DNA 05-NOV-02 1N5C TITLE CRYSTAL STRUCTURE ANALYSIS OF THE B-DNA DODECAMER CGCGAATT(ETHENOC)GCG COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(EDC)P*GP*CP*G)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS B FORM DOUBLE HELIX, 3, N4-ETHENO-2'-CYTIDINE MODIFICATION OPPOSITE KEYWDS 2 G, DNA EXPDTA X-RAY DIFFRACTION AUTHOR E.FREISINGER,A.FERNANDES,A.P.GROLLMAN,C.F.KISKER REVDAT 5 03-APR-24 1N5C 1 REMARK REVDAT 4 14-FEB-24 1N5C 1 REMARK LINK REVDAT 3 18-JAN-12 1N5C 1 VERSN HETATM HETSYN FORMUL REVDAT 3 2 1 REMARK REVDAT 2 24-FEB-09 1N5C 1 VERSN REVDAT 1 03-JUN-03 1N5C 0 JRNL AUTH E.FREISINGER,A.FERNANDES,A.P.GROLLMAN,C.F.KISKER JRNL TITL CRYSTALLOGRAPHIC CHARACTERIZATION OF AN EXOCYCLIC DNA JRNL TITL 2 ADDUCT: 3,N4-ETHENO-2'-DEOXYCYTIDINE IN THE DODECAMER JRNL TITL 3 5'-CGCGAATT(ETHENOC)GCG-3' JRNL REF J.MOL.BIOL. V. 329 685 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12787670 JRNL DOI 10.1016/S0022-2836(03)00445-5 REMARK 2 REMARK 2 RESOLUTION. 1.79 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) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT 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) : 0.164 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.161 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 200 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 3913 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.152 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.149 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 172 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 3141 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 245 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 73 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 303.75 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 137.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 1327 REMARK 3 NUMBER OF RESTRAINTS : 1445 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.020 REMARK 3 ANGLE DISTANCES (A) : 2.600 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.025 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.007 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.065 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.143 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: BABINET'S PRINCIPLE REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1N5C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-NOV-02. REMARK 100 THE DEPOSITION ID IS D_1000017537. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-00 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X26C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4113 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06100 REMARK 200 FOR THE DATA SET : 22.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.18700 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: ISOMORPHOUS REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NDB ENTRY BD0032 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DROP: MPD, POTASSIUM CHLORIDE, REMARK 280 SPERMINE TETRAHYDROCHLORIDE, CACODYLATE; RESERVOIR: MPD, PH 7.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K, PH 7.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 1 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -Y,-X,-Z+1/3 REMARK 290 5555 -X+Y,Y,-Z+2/3 REMARK 290 6555 X,X-Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.69600 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 33.84800 REMARK 290 SMTRY1 4 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 33.84800 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 67.69600 REMARK 290 SMTRY1 6 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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 300 REMARK: THE SECOND PART OF THE BIOLOGICAL ASSEMBLY/DOUBLE HELIX IS REMARK 300 GENERATED BY THE TWO FOLD AXIS: -X+Y+1, Y, -Z+3/2. 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 -1.000000 0.000000 0.000000 26.72300 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 67.69600 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 NA NA A1101 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1002 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1042 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1050 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1056 LIES ON A SPECIAL POSITION. 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 13 C6 - N1 - C2 ANGL. DEV. = -2.7 DEGREES REMARK 500 DC A 13 C2 - N3 - C4 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC A 13 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC A 13 N1 - C2 - O2 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG A 14 O4' - C1' - N9 ANGL. DEV. = -7.0 DEGREES REMARK 500 DT A 20 O4' - C1' - N1 ANGL. DEV. = -5.9 DEGREES REMARK 500 EDC A 21 C3' - O3' - P ANGL. DEV. = 11.2 DEGREES REMARK 500 DG A 22 N1 - C6 - O6 ANGL. DEV. = 4.9 DEGREES REMARK 500 DG A 22 C5 - C6 - O6 ANGL. DEV. = -5.1 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 NA A1101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC A 13 N3 REMARK 620 2 DC A 13 O2 56.8 REMARK 620 3 DG A 24 OP1 112.3 93.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1101 DBREF 1N5C A 13 24 PDB 1N5C 1N5C 13 24 SEQRES 1 A 12 DC DG DC DG DA DA DT DT EDC DG DC DG HET EDC A 21 21 HET NA A1101 1 HETNAM EDC N3,N4-ETHENO-2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM NA SODIUM ION HETSYN EDC 6-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO- HETSYN 2 EDC PENTOFURANOSYL)IMIDAZO[1,2-C]PYRIMIDIN-5(6H)-ONE FORMUL 1 EDC C11 H14 N3 O7 P FORMUL 2 NA NA 1+ FORMUL 3 HOH *73(H2 O) LINK O3' DT A 20 P EDC A 21 1555 1555 1.62 LINK O3' EDC A 21 P DG A 22 1555 1555 1.57 LINK N3 DC A 13 NA NA A1101 1555 1555 2.29 LINK O2 DC A 13 NA NA A1101 1555 1555 2.40 LINK OP1 DG A 24 NA NA A1101 5755 1555 2.28 SITE 1 AC1 3 DC A 13 DC A 23 DG A 24 CRYST1 26.723 26.723 101.544 90.00 90.00 120.00 P 32 1 2 6 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 0.037421 0.021605 0.000000 0.00000 SCALE2 0.000000 0.043210 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009848 0.00000