HEADER DNA 11-NOV-93 145D TITLE STRUCTURE AND THERMODYNAMICS OF NONALTERNATING C/G BASE PAIRS IN Z- TITLE 2 DNA: THE 1.3 ANGSTROMS CRYSTAL STRUCTURE OF THE ASYMMETRIC TITLE 3 HEXANUCLEOTIDE D(M(5)CGGGM(5) CG)/D(M(5)CGCCM(5)CG) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*(MCY)P*GP*GP*GP*(5CM)P*G)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*(MCY)P*GP*CP*CP*(5CM)P*G)-3'); COMPND 7 CHAIN: B, C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (5'-D(*(5CM)P*DGP*DGP*DGP*(5CM)P*DG)-3'); COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 SYNTHETIC: YES KEYWDS Z-DNA, DOUBLE HELIX, MODIFIED, DNA EXPDTA X-RAY DIFFRACTION AUTHOR G.P.SCHROTH,T.F.KAGAWA,P.SHING HO REVDAT 6 07-FEB-24 145D 1 LINK REVDAT 5 24-FEB-09 145D 1 VERSN REVDAT 4 01-APR-03 145D 1 JRNL REVDAT 3 28-JUN-02 145D 1 REMARK REVDAT 2 27-NOV-00 145D 5 REVDAT 1 15-JAN-94 145D 0 JRNL AUTH G.P.SCHROTH,T.F.KAGAWA,P.S.HO JRNL TITL STRUCTURE AND THERMODYNAMICS OF NONALTERNATING C.G BASE JRNL TITL 2 PAIRS IN Z-DNA: THE 1.3-A CRYSTAL STRUCTURE OF THE JRNL TITL 3 ASYMMETRIC HEXANUCLEOTIDE D(M5CGGGM5CG).D(M5CGCCM5CG). JRNL REF BIOCHEMISTRY V. 32 13381 1993 JRNL REFN ISSN 0006-2960 JRNL PMID 8257675 JRNL DOI 10.1021/BI00212A002 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.FUJII,A.H.-J.WANG,G.VAN DER MAREL,J.H.VAN BOOM,A.RICH REMARK 1 TITL MOLECULAR STRUCTURE OF (M5DC-DG)3: THE ROLE OF THE METHYL REMARK 1 TITL 2 GROUP ON 5-METHYL CYTOSINE IN STABILIZING Z-DNA REMARK 1 REF NUCLEIC ACIDS RES. V. 10 7879 1982 REMARK 1 REFN ISSN 0305-1048 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NUCLSQ REMARK 3 AUTHORS : WESTHOF,DUMAS,MORAS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.500 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 5029 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL 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) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 488 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 48 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 SUGAR-BASE BOND DISTANCE (A) : NULL ; NULL REMARK 3 SUGAR-BASE BOND ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 PHOSPHATE BONDS DISTANCE (A) : NULL ; NULL REMARK 3 PHOSPHATE BOND ANGLE, H-BOND (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION CONTACT (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION CONTACT (A) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 SUGAR-BASE BONDS (A**2) : NULL ; NULL REMARK 3 SUGAR-BASE ANGLES (A**2) : NULL ; NULL REMARK 3 PHOSPHATE BONDS (A**2) : NULL ; NULL REMARK 3 PHOSPHATE BOND ANGLE, H-BOND (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 145D 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_1000170104. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : SIEMENS 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 : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.00, VAPOR DIFFUSION 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 8.93250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.39850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.41100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.39850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 8.93250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 15.41100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 DBREF 145D A 1 6 PDB 145D 145D 1 6 DBREF 145D B 7 12 PDB 145D 145D 7 12 DBREF 145D C 13 18 PDB 145D 145D 13 18 DBREF 145D D 19 24 PDB 145D 145D 19 24 SEQRES 1 A 6 MCY DG DG DG 5CM DG SEQRES 1 B 6 MCY DG DC DC 5CM DG SEQRES 1 C 6 MCY DG DC DC 5CM DG SEQRES 1 D 6 5CM DG DG DG 5CM DG MODRES 145D MCY A 1 DC 5-METHYL-2'-DEOXYCYTIDINE MODRES 145D 5CM A 5 DC MODRES 145D MCY B 7 DC 5-METHYL-2'-DEOXYCYTIDINE MODRES 145D 5CM B 11 DC MODRES 145D MCY C 13 DC 5-METHYL-2'-DEOXYCYTIDINE MODRES 145D 5CM C 17 DC MODRES 145D 5CM D 19 DC MODRES 145D 5CM D 23 DC HET MCY A 1 31 HET 5CM A 5 33 HET MCY B 7 31 HET 5CM B 11 33 HET MCY C 13 31 HET 5CM C 17 33 HET 5CM D 19 31 HET 5CM D 23 33 HETNAM MCY 5-METHYL-2'-DEOXYCYTIDINE HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE FORMUL 1 MCY 3(C10 H15 N3 O4) FORMUL 1 5CM 5(C10 H16 N3 O7 P) FORMUL 5 HOH *48(H2 O) LINK O3'AMCY A 1 P A DG A 2 1555 1555 1.60 LINK O3'A DG A 4 P A5CM A 5 1555 1555 1.62 LINK O3'A5CM A 5 P A DG A 6 1555 1555 1.61 LINK O3'AMCY B 7 P A DG B 8 1555 1555 1.58 LINK O3'A DC B 10 P A5CM B 11 1555 1555 1.62 LINK O3'A5CM B 11 P A DG B 12 1555 1555 1.61 LINK O3'BMCY C 13 P B DG C 14 1555 1555 1.61 LINK O3'B DC C 16 P B5CM C 17 1555 1555 1.64 LINK O3'B5CM C 17 P B DG C 18 1555 1555 1.59 LINK O3'B5CM D 19 P B DG D 20 1555 1555 1.62 LINK O3'B DG D 22 P B5CM D 23 1555 1555 1.60 LINK O3'B5CM D 23 P B DG D 24 1555 1555 1.62 CRYST1 17.865 30.822 44.797 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 0.055975 0.000000 0.000000 0.00000 SCALE2 0.000000 0.032444 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022323 0.00000 HETATM 1 N1 AMCY A 1 15.435 17.853 19.106 0.65 8.96 N HETATM 2 C2 AMCY A 1 14.077 17.733 18.942 0.65 8.88 C HETATM 3 N3 AMCY A 1 13.329 18.839 18.830 0.65 8.48 N HETATM 4 C4 AMCY A 1 13.903 20.039 18.842 0.65 8.42 C HETATM 5 C5 AMCY A 1 15.322 20.196 18.987 0.65 8.59 C HETATM 6 C6 AMCY A 1 16.045 19.079 19.130 0.65 8.77 C HETATM 7 O2 AMCY A 1 13.523 16.653 18.834 0.65 8.82 O HETATM 8 N4 AMCY A 1 13.105 21.083 18.692 0.65 8.37 N HETATM 9 C1'AMCY A 1 16.192 16.602 19.214 0.65 9.41 C HETATM 10 C2'AMCY A 1 16.762 16.156 17.872 0.65 9.81 C HETATM 11 C3'AMCY A 1 17.881 15.244 18.348 0.65 10.32 C HETATM 12 C4'AMCY A 1 18.409 15.963 19.613 0.65 10.04 C HETATM 13 O4'AMCY A 1 17.351 16.844 20.012 0.65 9.62 O HETATM 14 O3'AMCY A 1 17.303 13.989 18.718 0.65 11.24 O HETATM 15 C5'AMCY A 1 19.763 16.691 19.435 0.65 10.15 C HETATM 16 O5'AMCY A 1 19.694 17.675 18.385 0.65 10.57 O HETATM 17 C5AAMCY A 1 15.964 21.583 18.943 0.65 8.75 C HETATM 18 H6 AMCY A 1 17.122 19.146 19.274 0.65 0.00 H HETATM 19 HN41AMCY A 1 13.481 22.025 18.675 0.65 15.00 H HETATM 20 HN42AMCY A 1 12.103 20.958 18.615 0.65 15.00 H HETATM 21 H1'AMCY A 1 15.578 15.798 19.620 0.65 0.00 H HETATM 22 H2'AMCY A 1 17.196 17.016 17.358 0.65 0.00 H HETATM 23 H2''AMCY A 1 16.022 15.668 17.235 0.65 0.00 H HETATM 24 H3'AMCY A 1 18.676 15.129 17.612 0.65 0.00 H HETATM 25 H4'AMCY A 1 18.519 15.229 20.410 0.65 0.00 H HETATM 26 H5'AMCY A 1 20.062 17.172 20.368 0.65 0.00 H HETATM 27 H5''AMCY A 1 20.513 15.946 19.166 0.65 0.00 H HETATM 28 HO5'AMCY A 1 18.781 17.979 18.358 0.65 15.00 H HETATM 29 H5A1AMCY A 1 16.650 21.626 18.102 0.65 0.00 H HETATM 30 H5A2AMCY A 1 16.499 21.759 19.875 0.65 0.00 H HETATM 31 H5A3AMCY A 1 15.221 22.363 18.816 0.65 0.00 H