HEADER DNA 24-MAR-16 5IYE 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, ZINC INTERACTIONS, DNA EXPDTA X-RAY DIFFRACTION AUTHOR S.KARTHIK,A.THIRUGNANASAMBANDAM,P.K.MANDAL,N.GAUTHAM REVDAT 5 08-NOV-23 5IYE 1 REMARK REVDAT 4 30-JAN-19 5IYE 1 REMARK REVDAT 3 06-DEC-17 5IYE 1 JRNL REVDAT 2 19-APR-17 5IYE 1 JRNL REVDAT 1 29-MAR-17 5IYE 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. 1.69 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) : 1.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.450 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 16056 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.910 REMARK 3 FREE R VALUE TEST SET COUNT : 1591 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 27.7955 - 3.7641 0.95 1257 139 0.1308 0.1505 REMARK 3 2 3.7641 - 2.9888 1.00 1335 140 0.1606 0.2175 REMARK 3 3 2.9888 - 2.6113 1.00 1341 154 0.2458 0.2674 REMARK 3 4 2.6113 - 2.3727 1.00 1342 142 0.2189 0.2386 REMARK 3 5 1.7484 - 1.6938 0.87 1179 132 0.2408 0.2542 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.71 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.45 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 : 0.013 636 REMARK 3 ANGLE : 1.553 978 REMARK 3 CHIRALITY : 0.078 110 REMARK 3 PLANARITY : 0.010 28 REMARK 3 DIHEDRAL : 14.044 272 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): 2.0752 14.2471 -2.5128 REMARK 3 T TENSOR REMARK 3 T11: 0.2813 T22: 0.3563 REMARK 3 T33: 0.3094 T12: -0.0476 REMARK 3 T13: 0.0108 T23: -0.0532 REMARK 3 L TENSOR REMARK 3 L11: -0.7336 L22: 0.9321 REMARK 3 L33: 0.8464 L12: -1.2092 REMARK 3 L13: -0.3319 L23: -0.8553 REMARK 3 S TENSOR REMARK 3 S11: -0.1788 S12: 0.1111 S13: -0.0728 REMARK 3 S21: -0.1690 S22: 0.4188 S23: -0.1728 REMARK 3 S31: 0.1296 S32: 0.0547 S33: 0.0219 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.0613 15.0277 2.0613 REMARK 3 T TENSOR REMARK 3 T11: 0.2747 T22: 0.3714 REMARK 3 T33: 0.3233 T12: 0.0461 REMARK 3 T13: -0.0100 T23: -0.0628 REMARK 3 L TENSOR REMARK 3 L11: -0.9652 L22: 0.7738 REMARK 3 L33: 0.6177 L12: 1.4515 REMARK 3 L13: 0.1571 L23: -0.8753 REMARK 3 S TENSOR REMARK 3 S11: -0.1552 S12: -0.1129 S13: 0.0909 REMARK 3 S21: 0.1955 S22: 0.4420 S23: -0.0910 REMARK 3 S31: -0.1736 S32: 0.0166 S33: 0.0537 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE ENTRY CONTAINS FRIEDEL PAIRS IN REMARK 3 F_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 5IYE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219623. 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) : 1.282 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 : XDS GPLV2 REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16064 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 REMARK 200 RESOLUTION RANGE LOW (A) : 27.792 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.7400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.27600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.690 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: HEXAGONAL SHAPED SINGLE LARGE CRYSTAL. REMARK 200 THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1MM DNA, 50MM SODIUM CACODYLATE REMARK 280 BUFFER, 8MM ZNCL2, 10MM SPERMINE, 40% MPD, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 44.10650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 22.05325 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 66.15975 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: 1650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 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 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 3 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC A 9 OP1 - P - OP2 ANGL. DEV. = 9.2 DEGREES REMARK 500 DC A 9 O5' - P - OP2 ANGL. DEV. = -7.5 DEGREES REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC B 3 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DT B 7 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA B 8 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC B 9 OP1 - P - OP2 ANGL. DEV. = 9.5 DEGREES REMARK 500 DC B 9 O5' - P - OP2 ANGL. DEV. = -7.0 DEGREES REMARK 500 DC B 9 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 13 N7 REMARK 620 2 HOH A 214 O 97.9 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5IYG RELATED DB: PDB REMARK 900 RELATED ID: 5IYJ RELATED DB: PDB DBREF 5IYE A 1 14 PDB 5IYE 5IYE 1 14 DBREF 5IYE B 1 14 PDB 5IYE 5IYE 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 HET ZN A 101 1 HET ZN B 101 1 HETNAM ZN ZINC ION FORMUL 3 ZN 2(ZN 2+) FORMUL 5 HOH *46(H2 O) LINK N7 DG A 13 ZN ZN A 101 1555 1555 2.56 LINK ZN ZN A 101 O HOH A 214 1555 1555 1.93 LINK ZN ZN B 101 O HOH B 213 1555 1555 2.47 SITE 1 AC1 2 DG A 13 HOH A 214 SITE 1 AC2 4 DG B 13 HOH B 207 HOH B 210 HOH B 213 CRYST1 29.283 29.283 88.213 90.00 90.00 90.00 P 41 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 0.034150 0.000000 0.000000 0.00000 SCALE2 0.000000 0.034150 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011336 0.00000