HEADER DNA 24-MAR-16 5IYJ TITLE COMPARISON OF X-RAY CRYSTAL STRUCTURES OF A TETRADECAMER SEQUENCE TITLE 2 D(CCCGGGTACCCGGG)2 AT 1.7 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*CP*GP*GP*GP*TP*AP*CP*CP*CP*GP*GP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS A-DNA DUPLEX, TETRAGONAL SPACE GROUP, DNA EXPDTA X-RAY DIFFRACTION AUTHOR S.KARTHIK,A.THIRUGNANASAMBANDAM,P.K.MANDAL,N.GAUTHAM REVDAT 5 08-NOV-23 5IYJ 1 REMARK REVDAT 4 30-JAN-19 5IYJ 1 REMARK REVDAT 3 06-DEC-17 5IYJ 1 JRNL REVDAT 2 19-APR-17 5IYJ 1 JRNL REVDAT 1 29-MAR-17 5IYJ 0 JRNL AUTH S.KARTHIK,A.THIRUGNANASAMBANDAM,P.K.MANDAL,N.GAUTHAM JRNL TITL COMPARISON OF X-RAY CRYSTAL STRUCTURES OF A TETRADECAMER JRNL TITL 2 SEQUENCE D(CCCGGGTACCCGGG)2 AT 1.7 ANGSTROM RESOLUTION. JRNL REF NUCLEOSIDES NUCLEOTIDES V. 36 343 2017 JRNL REF 2 NUCLEIC ACIDS JRNL REFN ISSN 1532-2335 JRNL PMID 28387634 JRNL DOI 10.1080/15257770.2017.1287378 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 9174 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 917 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 27.9507 - 3.2523 0.96 1244 137 0.1499 0.1587 REMARK 3 2 3.2523 - 2.5820 1.00 1197 134 0.2256 0.2736 REMARK 3 3 2.5820 - 2.2558 1.00 1179 131 0.2169 0.2699 REMARK 3 4 2.2558 - 2.0496 1.00 1178 130 0.2302 0.2816 REMARK 3 5 2.0496 - 1.9028 1.00 1140 127 0.2396 0.2759 REMARK 3 6 1.9028 - 1.7906 1.00 1169 131 0.2215 0.2328 REMARK 3 7 1.7906 - 1.7009 1.00 1150 127 0.2123 0.2657 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.52 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.019 636 REMARK 3 ANGLE : 1.798 978 REMARK 3 CHIRALITY : 0.087 110 REMARK 3 PLANARITY : 0.018 28 REMARK 3 DIHEDRAL : 16.101 272 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.6460 12.2164 -2.2514 REMARK 3 T TENSOR REMARK 3 T11: 0.2837 T22: 0.2699 REMARK 3 T33: 0.2941 T12: -0.0748 REMARK 3 T13: 0.0527 T23: -0.0228 REMARK 3 L TENSOR REMARK 3 L11: 0.7999 L22: 0.0959 REMARK 3 L33: 0.1659 L12: -1.5660 REMARK 3 L13: 1.0995 L23: -0.3303 REMARK 3 S TENSOR REMARK 3 S11: 0.1071 S12: -0.1684 S13: 0.0758 REMARK 3 S21: -0.2845 S22: 0.0682 S23: -0.0545 REMARK 3 S31: 0.0597 S32: 0.1279 S33: 0.0007 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.1316 12.8163 2.0687 REMARK 3 T TENSOR REMARK 3 T11: 0.2921 T22: 0.2982 REMARK 3 T33: 0.2956 T12: -0.0531 REMARK 3 T13: 0.0384 T23: -0.0457 REMARK 3 L TENSOR REMARK 3 L11: 0.1276 L22: 0.6864 REMARK 3 L33: 0.1836 L12: -1.5514 REMARK 3 L13: 0.5637 L23: -0.3815 REMARK 3 S TENSOR REMARK 3 S11: 0.0529 S12: -0.3769 S13: 0.1464 REMARK 3 S21: -0.1966 S22: 0.2026 S23: -0.1112 REMARK 3 S31: -0.1163 S32: -0.0929 S33: 0.0606 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5IYJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219650. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : SI(III) MONOCHROMATOR REMARK 200 OPTICS : BENT COLLIMATING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9182 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 29.403 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 41.2300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.40700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 10.12 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.5 REMARK 200 STARTING MODEL: 3V9D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1MM DNA, 50MM SODIUM CACODYLATE REMARK 280 BUFFER, 10MM SPERMINE, 25% MPD, PH 7.0, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.95300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 20.79150 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 20.79150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 22.47650 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 20.79150 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 20.79150 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 67.42950 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 20.79150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.79150 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 22.47650 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 20.79150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.79150 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 67.42950 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 44.95300 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL 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 DG A 6 N3 DG A 6 C4 -0.044 REMARK 500 DC B 3 O3' DC B 3 C3' -0.073 REMARK 500 DA B 8 O3' DA B 8 C3' -0.074 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 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG B 6 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA B 8 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC B 9 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG B 13 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5IYG RELATED DB: PDB REMARK 900 THE SAME OLIGONUCLEOTIDE SEQUENCE CO-CRYSTALLIZED WITH MAGNESIUM REMARK 900 CHLORIDE. REMARK 900 RELATED ID: 5IYE RELATED DB: PDB REMARK 900 THE SAME OLIGONUCLEOTIDE SEQUENCE COMPLEXED WITH ZINC LIGAND. DBREF 5IYJ A 1 14 PDB 5IYJ 5IYJ 1 14 DBREF 5IYJ B 1 14 PDB 5IYJ 5IYJ 1 14 SEQRES 1 A 14 DC DC DC DG DG DG DT DA DC DC DC DG DG SEQRES 2 A 14 DG SEQRES 1 B 14 DC DC DC DG DG DG DT DA DC DC DC DG DG SEQRES 2 B 14 DG FORMUL 3 HOH *57(H2 O) CRYST1 41.583 41.583 89.906 90.00 90.00 90.00 P 41 21 2 16 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 0.024048 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024048 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011123 0.00000