PDB Short entry for 2F8W HEADER DNA 04-DEC-05 2F8W TITLE CRYSTAL STRUCTURE OF D(CACGTG)2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*AP*CP*GP*TP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHETIC OLIGONUCLEOTIDE KEYWDS D(CACGTG), POLYAMINE, Z-DNA, 1, 3-PROPANEDIAMINE, DNA EXPDTA X-RAY DIFFRACTION AUTHOR N.NARAYANA,N.SHAMALA,K.N.GANESH,M.A.VISWAMITRA REVDAT 5 30-AUG-23 2F8W 1 REMARK REVDAT 4 18-APR-18 2F8W 1 REMARK REVDAT 3 04-APR-18 2F8W 1 REMARK REVDAT 2 24-FEB-09 2F8W 1 VERSN REVDAT 1 31-JAN-06 2F8W 0 JRNL AUTH N.NARAYANA,N.SHAMALA,K.N.GANESH,M.A.VISWAMITRA JRNL TITL INTERACTION BETWEEN THE Z-TYPE DNA DUPLEX AND JRNL TITL 2 1,3-PROPANEDIAMINE: CRYSTAL STRUCTURE OF D(CACGTG)2 AT 1.2 A JRNL TITL 3 RESOLUTION JRNL REF BIOCHEMISTRY V. 45 1200 2006 JRNL REFN ISSN 0006-2960 JRNL PMID 16430216 JRNL DOI 10.1021/BI051569L REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.EGLI,L.D.WILLIAMS,Q.GAO,A.RICH REMARK 1 TITL STRUCTURE OF THE PURE-SPERMINE FORM OF Z-DNA (MAGNESIUM REMARK 1 TITL 2 FREE) AT 1-RESOLUTION REMARK 1 REF BIOCHEMISTRY V. 30 11388 1991 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.THIYAGARAJAN,P.SATHEESH KUMAR,S.S.RAJAN,N.GAUTHAM REMARK 1 TITL STRUCTURE OF D(TGCGCA)2 AT 293 K: COMPARISON OF THE EFFECTS REMARK 1 TITL 2 OF SEQUENCE AND TEMPERATURE REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 58 1381 2002 REMARK 1 REFN ISSN 0907-4449 REMARK 1 REFERENCE 3 REMARK 1 AUTH C.SADASIVAN,N.GAUTHAM REMARK 1 TITL SEQUENCE-DEPENDENT MICROHETEROGENEITY OF Z-DNA: THE CRYSTAL REMARK 1 TITL 2 AND MOLECULAR STRUCTURES OF D(CACGCG).D(CGCGTG) AND REMARK 1 TITL 3 D(CGCACG).D(CGTGCG) REMARK 1 REF J.MOL.BIOL. V. 248 918 1995 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 4 REMARK 1 AUTH S.THIYAGARAJAN,S.S.RAJAN,N.GAUTHAM REMARK 1 TITL COBALT HEXAMMINE INDUCED TAUTOMERIC SHIFT IN Z-DNA: THE REMARK 1 TITL 2 STRUCTURE OF D(CGCGCA)*D(TGCGCG) IN TWO CRYSTAL FORMS REMARK 1 REF NUCLEIC ACIDS RES. V. 32 5945 2004 REMARK 1 REFN ISSN 0305-1048 REMARK 1 REFERENCE 5 REMARK 1 AUTH A.HARPER,J.A.BRANNIGAN,M.BUCK,L.HEWITT,R.J.LEWIS,M.H.MOORE, REMARK 1 AUTH 2 B.SCHNEIDER REMARK 1 TITL STRUCTURE OF D(TGCGCA)2 AND A COMPARISON TO OTHER DNA REMARK 1 TITL 2 HEXAMERS. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 54 1273 1998 REMARK 1 REFN ISSN 0907-4449 REMARK 1 REFERENCE 6 REMARK 1 AUTH M.COLL,I.FITA,J.LLOVERAS,J.A.SUBIRANA,F.BARDELLA, REMARK 1 AUTH 2 T.HUYNH-DINH,J.IGOLEN REMARK 1 TITL STRUCTURE OF D(CACGTG), Z-DNA HEXAMER CONTAINING AT BASE REMARK 1 TITL 2 PAIRS REMARK 1 REF NUCLEIC ACIDS RES. V. 16 8695 1988 REMARK 1 REFN ISSN 0305-1048 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 70.0 REMARK 3 NUMBER OF REFLECTIONS : 5687 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.500 REMARK 3 FREE R VALUE TEST SET COUNT : 93 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 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 : 19 REMARK 3 SOLVENT ATOMS : 71 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.80 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 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 3.180 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: X-PLOR REMARK 4 REMARK 4 2F8W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JAN-06. REMARK 100 THE DEPOSITION ID IS D_1000035597. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-FEB-87 REMARK 200 TEMPERATURE (KELVIN) : 291 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : ENRAF-NONIUS CAD4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CAD4 ASSOCIATED PROGRAM REMARK 200 DATA SCALING SOFTWARE : CAD4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5687 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 70.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04200 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1D48 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 7.5 MM SODIUM CACODYLATE, 2.5 MM REMARK 280 SRCL2, 2.5 MM SPERMINE, 50% ISOPROPANOL, PH 6.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K 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 9.21000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.59000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.37000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 21.59000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 9.21000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 15.37000 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A DUPLEX. THE COORDINATES REMARK 300 DEPOSITED WILL GENERATE THE BIOLOGICAL ASSEMBLY. THERE IS NO NEED REMARK 300 FOR SYMMETRY OPERATIONS TO GENERATE THE BIOLOGICAL ASSEMBLY. 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 44 O HOH B 66 2.09 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 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 DA A 2 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DT A 5 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC B 7 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC B 9 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT B 11 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT B 11 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DG B 12 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DA A 2 0.06 SIDE CHAIN REMARK 500 DG A 6 0.07 SIDE CHAIN REMARK 500 DC B 9 0.06 SIDE CHAIN REMARK 500 DG B 12 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 LIGAND Z5 IN THE MANUSCRIPT IS LABELED AS 13D IN THE REMARK 600 COORDINATE FILE. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SPM A 13 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 13D B 85 DBREF 2F8W A 1 6 PDB 2F8W 2F8W 1 6 DBREF 2F8W B 7 12 PDB 2F8W 2F8W 7 12 SEQRES 1 A 6 DC DA DC DG DT DG SEQRES 1 B 6 DC DA DC DG DT DG HET SPM A 13 14 HET 13D B 85 5 HETNAM SPM SPERMINE HETNAM 13D 1,3-DIAMINOPROPANE FORMUL 3 SPM C10 H26 N4 FORMUL 4 13D C3 H10 N2 FORMUL 5 HOH *71(H2 O) SITE 1 AC1 16 DA A 2 DC A 3 DG A 4 HOH A 17 SITE 2 AC1 16 HOH A 19 HOH A 36 HOH A 73 HOH A 80 SITE 3 AC1 16 DA B 8 DC B 9 DG B 10 DT B 11 SITE 4 AC1 16 DG B 12 HOH B 68 HOH B 69 HOH B 76 SITE 1 AC2 11 DG A 4 DT A 5 DG A 6 HOH A 46 SITE 2 AC2 11 HOH A 80 DC B 9 DG B 10 HOH B 47 SITE 3 AC2 11 HOH B 82 HOH B 83 HOH B 84 CRYST1 18.420 30.740 43.180 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 0.054290 0.000000 0.000000 0.00000 SCALE2 0.000000 0.032531 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023159 0.00000