HEADER DNA 15-JUL-98 417D TITLE A THYMINE-LIKE BASE ANALOGUE FORMS WOBBLE PAIRS WITH ADENINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*AP*CP*GP*(C46)P*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1 KEYWDS P.A BASE-PAIRS, PYRIMIDINE ANALOGUE, Z-DNA, DNA EXPDTA X-RAY DIFFRACTION AUTHOR P.K.T.LIN,M.H.SCHUERMAN,G.S.MOORE,L.VAN MEERVELT,D.LOAKES,D.M.BROWN, AUTHOR 2 M.H.MOORE REVDAT 5 03-APR-24 417D 1 REMARK REVDAT 4 28-FEB-24 417D 1 REMARK LINK REVDAT 3 24-FEB-09 417D 1 VERSN REVDAT 2 01-APR-03 417D 1 JRNL REVDAT 1 30-SEP-98 417D 0 JRNL AUTH G.S.SCHUERMAN,L.VAN MEERVELT,D.LOAKES,D.M.BROWN, JRNL AUTH 2 P.KONG THOO LIN,M.H.MOORE,S.A.SALISBURY JRNL TITL A THYMINE-LIKE BASE ANALOGUE FORMS WOBBLE PAIRS WITH ADENINE JRNL TITL 2 IN A Z-DNA DUPLEX. JRNL REF J.MOL.BIOL. V. 282 1005 1998 JRNL REFN ISSN 0022-2836 JRNL PMID 9753550 JRNL DOI 10.1006/JMBI.1998.2080 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-93 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 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 : CCP4 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.156 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.155 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 3920 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.150 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)) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 3696 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 244 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 58 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 : 2724 REMARK 3 NUMBER OF RESTRAINTS : 5294 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 ANGLE DISTANCES (A) : 0.014 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.020 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.041 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.083 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.020 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.058 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: BABINET'S PRINCIPLE REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : SHELXL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 417D 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_1000179217. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-OCT-95 REMARK 200 TEMPERATURE (KELVIN) : 150.00 REMARK 200 PH : 6.50 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 : BW7B 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 : CCP4 (AGROVATA, ROTAVATA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3920 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.0800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.10400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 11.92 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: PDB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE OBTAINED FROM A SOLUTION REMARK 280 THAT CONTAINED NA CACODYLATE, MG CHLORIDE, SPERMINE, MPD., PH REMARK 280 6.50, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277.00K 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 8.66900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.24300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.71600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.24300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 8.66900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 15.71600 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 1 C3' DC A 1 C2' -0.065 REMARK 500 DA A 2 C3' DA A 2 C2' -0.105 REMARK 500 DC A 3 C3' DC A 3 C2' -0.075 REMARK 500 DG A 4 C3' DG A 4 C2' -0.087 REMARK 500 DG A 6 C3' DG A 6 C2' -0.081 REMARK 500 DC B 7 C3' DC B 7 C2' -0.068 REMARK 500 DC B 7 O4' DC B 7 C4' -0.061 REMARK 500 DA B 8 C3' DA B 8 C2' -0.082 REMARK 500 DC B 9 C3' DC B 9 C2' -0.085 REMARK 500 DG B 10 C3' DG B 10 C2' -0.093 REMARK 500 DG B 12 C3' DG B 12 C2' -0.090 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 C2 - N3 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA A 2 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 DA A 2 O4' - C1' - N9 ANGL. DEV. = -6.5 DEGREES REMARK 500 DA A 2 C6 - N1 - C2 ANGL. DEV. = 4.0 DEGREES REMARK 500 DA A 2 N1 - C2 - N3 ANGL. DEV. = -4.5 DEGREES REMARK 500 DA A 2 C2 - N3 - C4 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA A 2 C5 - C6 - N1 ANGL. DEV. = -4.0 DEGREES REMARK 500 DC A 3 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 DG A 4 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 DG A 6 O4' - C4' - C3' ANGL. DEV. = -2.4 DEGREES REMARK 500 DG A 6 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC B 7 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DA B 8 O4' - C1' - N9 ANGL. DEV. = -4.3 DEGREES REMARK 500 DA B 8 C5 - C6 - N1 ANGL. DEV. = -3.4 DEGREES REMARK 500 DA B 8 C3' - O3' - P ANGL. DEV. = 12.0 DEGREES REMARK 500 DC B 9 OP1 - P - OP2 ANGL. DEV. = -10.5 DEGREES REMARK 500 DC B 9 O4' - C1' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 DC B 9 C6 - N1 - C2 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC B 9 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 DG B 12 O4' - C1' - N9 ANGL. DEV. = -6.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 417D A 1 6 PDB 417D 417D 1 6 DBREF 417D B 7 12 PDB 417D 417D 7 12 SEQRES 1 A 6 DC DA DC DG C46 DG SEQRES 1 B 6 DC DA DC DG C46 DG MODRES 417D C46 A 5 DC MODRES 417D C46 B 11 DC HET C46 A 5 22 HET C46 B 11 22 HETNAM C46 6H,8H-3,4-DIHYDROPYRIMIDO[4,5-C][1,2]OXAZIN-7- HETNAM 2 C46 0NE(CYTIDINE)-5'-MONOPHOSPHATE FORMUL 1 C46 2(C11 H16 N3 O8 P) FORMUL 3 HOH *58(H2 O) LINK O3' DG A 4 P C46 A 5 1555 1555 1.60 LINK O3' C46 A 5 P DG A 6 1555 1555 1.61 LINK O3' DG B 10 P C46 B 11 1555 1555 1.61 LINK O3' C46 B 11 P DG B 12 1555 1555 1.61 CRYST1 17.338 31.432 44.486 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 0.057677 0.000000 0.000000 0.00000 SCALE2 0.000000 0.031815 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022479 0.00000