HEADER DNA 18-AUG-25 9Q3D TITLE [20-7B C|A] 20 BP TENSEGRITY TRIANGLE THAT PROPAGATES VIA BLUNT-END TITLE 2 STACKING WITH C STACKING ON A AT THE INTERFACE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*CP*GP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*GP*TP*CP*A)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*CP*CP*GP*TP*AP*CP*A)-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(*GP*GP*CP*TP*CP*G)-3'); COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: DNA (5'-D(*TP*GP*AP*CP*TP*GP*T)-3'); COMPND 16 CHAIN: D; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 4; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630 KEYWDS TENSEGRITY TRIANGLE, BLUNT, DNA EXPDTA X-RAY DIFFRACTION AUTHOR A.HORVATH,K.WOLOSZYN,S.VECCHIONI,Y.P.OHAYON,R.SHA REVDAT 1 05-NOV-25 9Q3D 0 JRNL AUTH A.HORVATH,K.WOLOSZYN,S.VECCHIONI,Y.P.OHAYON,R.SHA JRNL TITL BLUNTED TENSEGRITY TRIANGLES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 5.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 5.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 2198 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.281 REMARK 3 R VALUE (WORKING SET) : 0.281 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 111 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 54.3000 - 5.0300 1.00 2087 111 0.2805 0.2837 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) : 0.000 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.438 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 147.1 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 178.4 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 : 0.007 904 REMARK 3 ANGLE : 1.007 1388 REMARK 3 CHIRALITY : 0.056 156 REMARK 3 PLANARITY : 0.006 40 REMARK 3 DIHEDRAL : 39.339 416 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 103 THROUGH 122) REMARK 3 ORIGIN FOR THE GROUP (A): -47.6964 30.0043 -4.5920 REMARK 3 T TENSOR REMARK 3 T11: 3.1852 T22: 0.0557 REMARK 3 T33: 3.4887 T12: -0.2385 REMARK 3 T13: -1.7771 T23: 1.0528 REMARK 3 L TENSOR REMARK 3 L11: 0.9044 L22: 1.8763 REMARK 3 L33: 1.2294 L12: -0.7352 REMARK 3 L13: 0.2016 L23: -1.5008 REMARK 3 S TENSOR REMARK 3 S11: 0.5711 S12: 0.2839 S13: -0.8055 REMARK 3 S21: -0.7381 S22: 0.0621 S23: 0.0059 REMARK 3 S31: 1.7298 S32: 0.2783 S33: 0.4826 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 119 THROUGH 125) REMARK 3 ORIGIN FOR THE GROUP (A): -50.5436 29.0163 -4.3221 REMARK 3 T TENSOR REMARK 3 T11: -0.2464 T22: 1.2991 REMARK 3 T33: 0.7574 T12: 0.9072 REMARK 3 T13: -1.1616 T23: -1.2156 REMARK 3 L TENSOR REMARK 3 L11: 0.3458 L22: 0.2592 REMARK 3 L33: 0.2482 L12: 0.0018 REMARK 3 L13: -0.2882 L23: 0.0774 REMARK 3 S TENSOR REMARK 3 S11: 0.2536 S12: 0.2434 S13: -0.0067 REMARK 3 S21: -0.1415 S22: -0.0483 S23: -0.2812 REMARK 3 S31: 0.4199 S32: -0.4474 S33: 0.8605 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'C' AND RESID 209 THROUGH 214) REMARK 3 ORIGIN FOR THE GROUP (A): -56.8823 11.3144 -17.6886 REMARK 3 T TENSOR REMARK 3 T11: 1.8837 T22: 0.8414 REMARK 3 T33: 3.0326 T12: -0.3221 REMARK 3 T13: 1.6077 T23: -1.0840 REMARK 3 L TENSOR REMARK 3 L11: 1.3634 L22: 1.3966 REMARK 3 L33: 1.2367 L12: 0.9439 REMARK 3 L13: -0.4957 L23: 0.0124 REMARK 3 S TENSOR REMARK 3 S11: -0.2853 S12: 0.1530 S13: -0.3524 REMARK 3 S21: -0.2479 S22: 0.0686 S23: -0.2244 REMARK 3 S31: 0.0657 S32: -0.1822 S33: -0.2253 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN 'D' AND RESID 202 THROUGH 208) REMARK 3 ORIGIN FOR THE GROUP (A): -40.6970 46.1117 5.9118 REMARK 3 T TENSOR REMARK 3 T11: 2.2415 T22: 1.3645 REMARK 3 T33: 2.5871 T12: -0.6312 REMARK 3 T13: -1.5073 T23: -0.6257 REMARK 3 L TENSOR REMARK 3 L11: 0.5412 L22: 0.2978 REMARK 3 L33: 1.1494 L12: 0.3784 REMARK 3 L13: 0.3537 L23: 0.0805 REMARK 3 S TENSOR REMARK 3 S11: 0.1276 S12: -0.6037 S13: -0.0113 REMARK 3 S21: 0.5440 S22: -0.2077 S23: -0.4620 REMARK 3 S31: -0.0082 S32: 0.2549 S33: -0.5763 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 9Q3D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1000299122. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.007430 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : STARANISO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2202 REMARK 200 RESOLUTION RANGE HIGH (A) : 5.030 REMARK 200 RESOLUTION RANGE LOW (A) : 62.695 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 19.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 5.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 5.05 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 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MOPS, 1.25 M MAGNESIUM SULFATE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-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 -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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 27.67000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 27.67000 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 27.67000 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: DODECAMERIC 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 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 -62.69500 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 108.59093 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -125.39000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 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 DT A 111 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC A 121 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT B 122 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC B 124 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DT C 212 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT D 202 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 9Q3D A 103 122 PDB 9Q3D 9Q3D 103 122 DBREF 9Q3D B 119 125 PDB 9Q3D 9Q3D 119 125 DBREF 9Q3D C 209 214 PDB 9Q3D 9Q3D 209 214 DBREF 9Q3D D 202 208 PDB 9Q3D 9Q3D 202 208 SEQRES 1 A 20 DC DG DA DG DC DC DT DG DT DA DC DG DG SEQRES 2 A 20 DA DC DA DG DT DC DA SEQRES 1 B 7 DC DC DG DT DA DC DA SEQRES 1 C 6 DG DG DC DT DC DG SEQRES 1 D 7 DT DG DA DC DT DG DT CRYST1 125.390 125.390 55.340 90.00 90.00 120.00 P 63 6 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 0.007975 0.004604 0.000000 0.00000 SCALE2 0.000000 0.009209 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018070 0.00000 MASTER 287 0 0 0 0 0 0 6 808 4 0 5 END