HEADER DNA 29-MAY-25 9V87 TITLE CRYSTAL STRUCTURE OF D(CGTTAACG)2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*CP*GP*TP*TP*AP*AP*CP*G)-3'); COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS DNA PERFECTLY MATCHED, WATSON AND CRICK BASE PAIRING, DNA EXPDTA X-RAY DIFFRACTION AUTHOR Y.C.YUAN,S.C.WANG,M.H.HOU REVDAT 1 03-JUN-26 9V87 0 JRNL AUTH Y.C.YUAN,S.C.WANG,M.H.HOU JRNL TITL CRYSTAL STRUCTURE OF D(CGTTAACG)2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.21.1_5286: ???) 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 : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 11122 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.257 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.960 REMARK 3 FREE R VALUE TEST SET COUNT : 1108 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 18.9700 - 3.2200 0.89 1291 141 0.1698 0.2412 REMARK 3 2 3.2100 - 2.5500 0.90 1258 140 0.2436 0.2642 REMARK 3 3 2.5500 - 2.2300 0.90 1255 140 0.2969 0.3096 REMARK 3 4 2.2300 - 2.0300 0.90 1250 139 0.2983 0.3520 REMARK 3 5 2.0300 - 1.8800 0.90 1237 134 0.3483 0.3351 REMARK 3 6 1.8800 - 1.7700 0.90 1248 140 0.3900 0.3417 REMARK 3 7 1.7700 - 1.6800 0.90 1221 134 0.3864 0.3952 REMARK 3 8 1.6800 - 1.6100 0.90 1255 139 0.4271 0.4225 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.490 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 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 : 0.008 695 REMARK 3 ANGLE : 0.838 1048 REMARK 3 CHIRALITY : 0.045 116 REMARK 3 PLANARITY : 0.005 29 REMARK 3 DIHEDRAL : 32.529 332 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 9V87 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JUN-25. REMARK 100 THE DEPOSITION ID IS D_1300058293. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL15A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11151 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.610 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.34200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.6MM OLIGONUCLEOTIDE, 50MM HEPES PH REMARK 280 7.5, 2MM SPERMINE TETRAHYDROCHLORIDE, 8.5MM COBALT(II) CHLORIDE, REMARK 280 5% MPD, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 1 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -Y,-X,-Z+2/3 REMARK 290 5555 -X+Y,Y,-Z+1/3 REMARK 290 6555 X,X-Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.78400 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 47.56800 REMARK 290 SMTRY1 4 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 47.56800 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 23.78400 REMARK 290 SMTRY1 6 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CL CL B 103 LIES ON A SPECIAL POSITION. REMARK 375 CO CO C 202 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 204 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 207 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 211 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 215 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 211 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 308 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 318 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 DC B 1 REMARK 465 DC C 1 REMARK 465 DC D 1 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 CO B 101 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 8 N7 REMARK 620 2 HOH B 205 O 89.3 REMARK 620 3 HOH B 206 O 83.0 85.0 REMARK 620 4 HOH D 206 O 86.8 170.9 102.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO C 203 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG C 2 N7 REMARK 620 2 HOH C 317 O 96.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO C 202 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG C 8 N7 REMARK 620 2 DG C 8 N7 0.0 REMARK 620 3 HOH C 302 O 88.5 88.5 REMARK 620 4 HOH C 302 O 91.1 91.1 146.5 REMARK 620 5 HOH C 308 O 93.9 93.9 106.6 106.8 REMARK 620 6 HOH C 308 O 93.9 93.9 106.6 106.9 0.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO D 101 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG D 2 N7 REMARK 620 2 HOH D 209 O 105.4 REMARK 620 3 HOH D 215 O 147.2 105.1 REMARK 620 N 1 2 DBREF 9V87 A 1 8 PDB 9V87 9V87 1 8 DBREF 9V87 B 1 8 PDB 9V87 9V87 1 8 DBREF 9V87 C 1 8 PDB 9V87 9V87 1 8 DBREF 9V87 D 1 8 PDB 9V87 9V87 1 8 SEQRES 1 A 8 DC DG DT DT DA DA DC DG SEQRES 1 B 8 DC DG DT DT DA DA DC DG SEQRES 1 C 8 DC DG DT DT DA DA DC DG SEQRES 1 D 8 DC DG DT DT DA DA DC DG HET SPK A 101 14 HET CO A 102 1 HET CO B 101 1 HET CO B 102 1 HET CL B 103 1 HET SPK C 201 14 HET CO C 202 1 HET CO C 203 1 HET CO D 101 1 HET CO D 102 1 HETNAM SPK SPERMINE (FULLY PROTONATED FORM) HETNAM CO COBALT (II) ION HETNAM CL CHLORIDE ION FORMUL 5 SPK 2(C10 H30 N4 4+) FORMUL 6 CO 7(CO 2+) FORMUL 9 CL CL 1- FORMUL 15 HOH *66(H2 O) LINK N7 DG A 2 CO CO A 102 1555 1555 2.11 LINK N7 DG B 2 CO CO B 102 1555 1555 1.92 LINK N7 DG B 8 CO CO B 101 1555 1555 2.09 LINK CO CO B 101 O HOH B 205 1555 1555 1.97 LINK CO CO B 101 O HOH B 206 1555 1555 2.28 LINK CO CO B 101 O HOH D 206 1555 6545 1.91 LINK N7 DG C 2 CO CO C 203 1555 1555 2.21 LINK N7 DG C 8 CO CO C 202 1555 1555 2.30 LINK N7 DG C 8 CO CO C 202 1555 4554 2.35 LINK CO CO C 202 O HOH C 302 1555 1555 1.98 LINK CO CO C 202 O HOH C 302 1555 4554 1.97 LINK CO CO C 202 O HOH C 308 1555 1555 2.19 LINK CO CO C 202 O HOH C 308 1555 4554 2.19 LINK CO CO C 203 O HOH C 317 1555 1555 1.93 LINK N7 DG D 2 CO CO D 101 1555 1555 1.99 LINK CO CO D 101 O HOH D 209 1555 1555 2.03 LINK CO CO D 101 O HOH D 215 1555 1555 1.95 CRYST1 45.447 45.447 71.352 90.00 90.00 120.00 P 31 1 2 24 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 0.022004 0.012704 0.000000 0.00000 SCALE2 0.000000 0.025408 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014015 0.00000 CONECT 33 618 CONECT 179 620 CONECT 302 619 CONECT 325 637 CONECT 448 636 CONECT 471 638 CONECT 604 605 CONECT 605 604 606 CONECT 606 605 607 CONECT 607 606 608 CONECT 608 607 609 CONECT 609 608 610 CONECT 610 609 611 CONECT 611 610 612 CONECT 612 611 613 CONECT 613 612 614 CONECT 614 613 615 CONECT 615 614 616 CONECT 616 615 617 CONECT 617 616 CONECT 618 33 CONECT 619 302 660 661 CONECT 620 179 CONECT 622 623 CONECT 623 622 624 CONECT 624 623 625 CONECT 625 624 626 CONECT 626 625 627 CONECT 627 626 628 CONECT 628 627 629 CONECT 629 628 630 CONECT 630 629 631 CONECT 631 630 632 CONECT 632 631 633 CONECT 633 632 634 CONECT 634 633 635 CONECT 635 634 CONECT 636 448 668 674 CONECT 637 325 683 CONECT 638 471 697 703 CONECT 660 619 CONECT 661 619 CONECT 668 636 CONECT 674 636 CONECT 683 637 CONECT 697 638 CONECT 703 638 MASTER 268 0 10 0 0 0 0 6 701 4 47 4 END