HEADER DNA 20-AUG-97 362D TITLE THE STRUCTURE OF D(TGCGCA)2 AND A COMPARISON TO OTHER Z-DNA HEXAMERS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*GP*CP*GP*CP*A)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS Z-DNA, DOUBLE HELIX, DNA EXPDTA X-RAY DIFFRACTION AUTHOR N.A.HARPER,J.A.BRANNIGAN,M.BUCK,R.J.LEWIS,M.H.MOORE,B.SCHNEIDER REVDAT 4 02-AUG-23 362D 1 REMARK REVDAT 3 24-FEB-09 362D 1 VERSN REVDAT 2 01-APR-03 362D 1 JRNL REVDAT 1 20-NOV-97 362D 0 SPRSDE 18-NOV-97 362D 347D JRNL AUTH A.HARPER,J.A.BRANNIGAN,M.BUCK,L.HEWITT,R.J.LEWIS,M.H.MOORE, JRNL AUTH 2 B.SCHNEIDER JRNL TITL STRUCTURE OF D(TGCGCA)2 AND A COMPARISON TO OTHER DNA JRNL TITL 2 HEXAMERS. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 54 1273 1998 JRNL REFN ISSN 0907-4449 JRNL PMID 10089504 JRNL DOI 10.1107/S0907444998002807 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-96 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : NULL 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) : 0.117 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.120 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.173 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 695 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 7005 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)) : NULL 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)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 240 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 78 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 332.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 138.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 1 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 3018 REMARK 3 NUMBER OF RESTRAINTS : 2782 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.000 REMARK 3 ANGLE DISTANCES (A) : 0.000 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.000 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.016 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.022 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.065 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESTRAINED ANISOTROPIC REFINEMENT OF REMARK 3 NON-HYDROGEN ATOMS. ANISOTROPIC REFINEMENT REDUCED FREE R (NO REMARK 3 CUTOFF) BY 1.4%. REMARK 4 REMARK 4 362D 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_1000178832. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-SEP-95 REMARK 200 TEMPERATURE (KELVIN) : 120.00 REMARK 200 PH : 6.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 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 : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7024 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 24.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.07800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 23.60 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: MODIFIED NDB ENTRY ZDF002 (PDB ENTRY 1DCG) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.00 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 10.58100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.16750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 14.33500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.16750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 10.58100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 14.33500 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 DT A 1 C5' DT A 1 C4' 0.070 REMARK 500 DT A 1 O3' DT A 1 C3' 0.115 REMARK 500 DG A 2 C5' DG A 2 C4' 0.044 REMARK 500 DG A 2 O3' DG A 2 C3' 0.078 REMARK 500 DG A 2 N1 DG A 2 C2 0.055 REMARK 500 DG A 2 N7 DG A 2 C8 -0.050 REMARK 500 DG A 2 C8 DG A 2 N9 0.052 REMARK 500 DG A 2 C6 DG A 2 O6 0.056 REMARK 500 DC A 3 C4 DC A 3 N4 0.065 REMARK 500 DC A 3 C4 DC A 3 C5 -0.068 REMARK 500 DC A 3 C5 DC A 3 C6 0.064 REMARK 500 DG A 4 O3' DG A 4 C3' 0.079 REMARK 500 DG A 4 N3 DG A 4 C4 0.055 REMARK 500 DG A 4 N7 DG A 4 C8 -0.038 REMARK 500 DC A 5 N3 DC A 5 C4 0.047 REMARK 500 DA A 6 C5' DA A 6 C4' 0.046 REMARK 500 DA A 6 C2' DA A 6 C1' -0.063 REMARK 500 DA A 6 N3 DA A 6 C4 0.079 REMARK 500 DA A 6 C4 DA A 6 C5 -0.069 REMARK 500 DA A 6 C6 DA A 6 N1 0.059 REMARK 500 DT B 7 C5 DT B 7 C7 0.104 REMARK 500 DG B 8 C5 DG B 8 C6 0.069 REMARK 500 DC B 9 N1 DC B 9 C6 0.054 REMARK 500 DC B 9 C2 DC B 9 N3 0.069 REMARK 500 DG B 10 N3 DG B 10 C4 0.058 REMARK 500 DG B 10 C4 DG B 10 C5 0.046 REMARK 500 DG B 10 C6 DG B 10 N1 0.059 REMARK 500 DG B 10 C5 DG B 10 N7 0.042 REMARK 500 DG B 10 N7 DG B 10 C8 0.075 REMARK 500 DG B 10 O3' DC B 11 P 0.168 REMARK 500 DC B 11 P DC B 11 O5' -0.103 REMARK 500 DC B 11 P DC B 11 O5' 0.164 REMARK 500 DA B 12 C5 DA B 12 N7 0.052 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 DT A 1 O5' - C5' - C4' ANGL. DEV. = -5.9 DEGREES REMARK 500 DT A 1 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT A 1 C6 - N1 - C2 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT A 1 N1 - C2 - N3 ANGL. DEV. = 4.4 DEGREES REMARK 500 DT A 1 C2 - N3 - C4 ANGL. DEV. = -4.0 DEGREES REMARK 500 DT A 1 C5 - C6 - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 DT A 1 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 DG A 2 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG A 2 N1 - C2 - N2 ANGL. DEV. = -7.0 DEGREES REMARK 500 DG A 2 N3 - C2 - N2 ANGL. DEV. = 7.1 DEGREES REMARK 500 DG A 2 C5 - C6 - O6 ANGL. DEV. = -3.8 DEGREES REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC A 3 C6 - N1 - C2 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC A 3 C2 - N3 - C4 ANGL. DEV. = -3.4 DEGREES REMARK 500 DC A 3 N3 - C4 - C5 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC A 3 C5 - C6 - N1 ANGL. DEV. = -4.8 DEGREES REMARK 500 DG A 4 C4 - C5 - N7 ANGL. DEV. = -2.5 DEGREES REMARK 500 DG A 4 C5 - N7 - C8 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA A 6 C5' - C4' - C3' ANGL. DEV. = -11.0 DEGREES REMARK 500 DA A 6 C3' - C2' - C1' ANGL. DEV. = 7.3 DEGREES REMARK 500 DA A 6 C4 - C5 - C6 ANGL. DEV. = 7.1 DEGREES REMARK 500 DA A 6 C5 - C6 - N1 ANGL. DEV. = -5.4 DEGREES REMARK 500 DA A 6 C6 - C5 - N7 ANGL. DEV. = -7.1 DEGREES REMARK 500 DT B 7 C6 - N1 - C2 ANGL. DEV. = -6.1 DEGREES REMARK 500 DT B 7 C2 - N3 - C4 ANGL. DEV. = 5.9 DEGREES REMARK 500 DT B 7 N3 - C4 - C5 ANGL. DEV. = -5.3 DEGREES REMARK 500 DT B 7 N1 - C2 - O2 ANGL. DEV. = -6.3 DEGREES REMARK 500 DT B 7 N3 - C2 - O2 ANGL. DEV. = 4.8 DEGREES REMARK 500 DT B 7 N3 - C4 - O4 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG B 8 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG B 8 C4 - C5 - N7 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG B 8 C5 - N7 - C8 ANGL. DEV. = -3.8 DEGREES REMARK 500 DG B 8 C6 - C5 - N7 ANGL. DEV. = -5.1 DEGREES REMARK 500 DC B 9 O4' - C4' - C3' ANGL. DEV. = 3.9 DEGREES REMARK 500 DG B 10 O4' - C1' - N9 ANGL. DEV. = -4.5 DEGREES REMARK 500 DG B 10 N1 - C2 - N3 ANGL. DEV. = 5.3 DEGREES REMARK 500 DG B 10 N3 - C4 - C5 ANGL. DEV. = -3.6 DEGREES REMARK 500 DG B 10 C4 - C5 - C6 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG B 10 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 DC B 11 O3' - P - OP1 ANGL. DEV. = 10.7 DEGREES REMARK 500 DC B 11 O5' - P - OP2 ANGL. DEV. = 8.5 DEGREES REMARK 500 DC B 11 O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES REMARK 500 DC B 11 N3 - C4 - C5 ANGL. DEV. = -3.4 DEGREES REMARK 500 DC B 11 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA B 12 C2 - N3 - C4 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA B 12 N9 - C4 - C5 ANGL. DEV. = 2.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 13 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 14 DBREF 362D A 1 6 PDB 362D 362D 1 6 DBREF 362D B 7 12 PDB 362D 362D 7 12 SEQRES 1 A 6 DT DG DC DG DC DA SEQRES 1 B 6 DT DG DC DG DC DA HET NCO A 13 7 HET NCO A 14 7 HETNAM NCO COBALT HEXAMMINE(III) FORMUL 3 NCO 2(CO H18 N6 3+) FORMUL 5 HOH *78(H2 O) SITE 1 AC1 9 DG A 4 DA A 6 NCO A 14 HOH A 29 SITE 2 AC1 9 HOH A 44 HOH A 71 DA B 12 HOH B 32 SITE 3 AC1 9 HOH B 74 SITE 1 AC2 9 DC A 3 DG A 4 NCO A 13 HOH A 49 SITE 2 AC2 9 DG B 8 DC B 9 HOH B 23 HOH B 33 SITE 3 AC2 9 HOH B 54 CRYST1 21.162 28.670 44.335 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 0.047255 0.000000 0.000000 0.00000 SCALE2 0.000000 0.034880 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022556 0.00000