HEADER DNA 17-JUL-25 9PMG TITLE [22-7B G|T] 22 BP TENSEGRITY TRIANGLE THAT PROPAGATES VIA BLUNT-END TITLE 2 STACKING WITH G STACKING ON T AT THE INTERFACE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*GP*GP*AP*TP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*GP*AP*TP*CP*T)- COMPND 4 3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*CP*CP*GP*TP*AP*CP*A)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(P*GP*GP*CP*AP*TP*CP*C)-3'); COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA (5'-D(*AP*GP*AP*TP*CP*TP*GP*T)-3'); COMPND 17 CHAIN: D; COMPND 18 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 DNA, TENSEGRITY TRIANGLE, BLUNT, STACKING EXPDTA X-RAY DIFFRACTION AUTHOR A.HORVATH,K.WOLOSZYN,S.VECCHIONI,Y.P.OHAYON,R.SHA REVDAT 1 05-NOV-25 9PMG 0 JRNL AUTH A.HORVATH,K.WOLOSZYN,S.VECCHIONI,Y.P.OHAYON,R.SHA JRNL TITL BLUNT-END TENSEGRITY TRIANGLES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 5.68 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) : 5.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 79.8 REMARK 3 NUMBER OF REFLECTIONS : 1554 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.125 REMARK 3 R VALUE (WORKING SET) : 0.122 REMARK 3 FREE R VALUE : 0.164 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.720 REMARK 3 FREE R VALUE TEST SET COUNT : 151 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 38.4300 - 5.6800 0.80 1403 151 0.1215 0.1637 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) : 21.123 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 428.8 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 366.5 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 : 0.011 999 REMARK 3 ANGLE : 1.108 1534 REMARK 3 CHIRALITY : 0.065 173 REMARK 3 PLANARITY : 0.006 44 REMARK 3 DIHEDRAL : 39.179 463 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 102 THROUGH 123) REMARK 3 ORIGIN FOR THE GROUP (A): 52.9258 -29.0333 1.3224 REMARK 3 T TENSOR REMARK 3 T11: 3.5890 T22: 2.5693 REMARK 3 T33: 2.0033 T12: 0.4695 REMARK 3 T13: 0.4036 T23: 0.1215 REMARK 3 L TENSOR REMARK 3 L11: 6.0260 L22: 2.0723 REMARK 3 L33: 5.7350 L12: 2.0416 REMARK 3 L13: 2.1351 L23: 5.1749 REMARK 3 S TENSOR REMARK 3 S11: 0.8455 S12: 0.1256 S13: 0.5876 REMARK 3 S21: -0.1870 S22: -0.2128 S23: 5.4467 REMARK 3 S31: -0.6882 S32: 0.3152 S33: 0.0857 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 119 THROUGH 125) REMARK 3 ORIGIN FOR THE GROUP (A): 54.1792 -31.5958 1.4183 REMARK 3 T TENSOR REMARK 3 T11: 6.1156 T22: 4.2962 REMARK 3 T33: 1.6233 T12: 1.1696 REMARK 3 T13: 0.2976 T23: 0.4085 REMARK 3 L TENSOR REMARK 3 L11: 6.1545 L22: 2.0028 REMARK 3 L33: 0.6561 L12: 2.8292 REMARK 3 L13: 0.3953 L23: -2.3340 REMARK 3 S TENSOR REMARK 3 S11: 2.6524 S12: 0.8503 S13: 1.7165 REMARK 3 S21: -1.9146 S22: -1.0971 S23: 0.5345 REMARK 3 S31: -6.1482 S32: -7.3921 S33: -2.0098 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'C' AND RESID 209 THROUGH 215) REMARK 3 ORIGIN FOR THE GROUP (A): 41.2525 -45.1353 14.1485 REMARK 3 T TENSOR REMARK 3 T11: 3.7756 T22: 3.7006 REMARK 3 T33: 3.8974 T12: -0.8472 REMARK 3 T13: -1.1562 T23: 1.4586 REMARK 3 L TENSOR REMARK 3 L11: 8.5886 L22: 5.4130 REMARK 3 L33: 1.9925 L12: 5.5499 REMARK 3 L13: 8.3442 L23: 7.3956 REMARK 3 S TENSOR REMARK 3 S11: 0.1995 S12: -4.5114 S13: 3.0710 REMARK 3 S21: -2.7483 S22: -3.1785 S23: -0.3335 REMARK 3 S31: -1.9590 S32: 1.1620 S33: -4.0467 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN 'D' AND RESID 201 THROUGH 208) REMARK 3 ORIGIN FOR THE GROUP (A): 62.2857 -12.5951 -10.1527 REMARK 3 T TENSOR REMARK 3 T11: 5.3008 T22: 4.1036 REMARK 3 T33: 4.9793 T12: -1.4033 REMARK 3 T13: 1.0544 T23: -0.2229 REMARK 3 L TENSOR REMARK 3 L11: 8.0677 L22: 5.3193 REMARK 3 L33: 8.6956 L12: 2.2134 REMARK 3 L13: -2.1032 L23: 5.6102 REMARK 3 S TENSOR REMARK 3 S11: -2.7343 S12: 3.2496 S13: 7.2125 REMARK 3 S21: 0.4353 S22: 6.8294 S23: 1.6477 REMARK 3 S31: -4.2625 S32: 3.4479 S33: 4.5812 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 9PMG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1000298115. 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 : 1570 REMARK 200 RESOLUTION RANGE HIGH (A) : 5.680 REMARK 200 RESOLUTION RANGE LOW (A) : 66.567 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.9 REMARK 200 DATA REDUNDANCY : 19.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 5.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 6.31 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 31.39200 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 31.39200 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 31.39200 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 66.56650 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -115.29656 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 133.13300 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 DC A 107 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC A 108 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG A 110 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC A 117 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG A 119 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DG C 209 O4' - C4' - C3' ANGL. DEV. = -3.3 DEGREES REMARK 500 DG C 209 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC C 215 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 9PMG A 102 123 PDB 9PMG 9PMG 102 123 DBREF 9PMG B 119 125 PDB 9PMG 9PMG 119 125 DBREF 9PMG C 209 215 PDB 9PMG 9PMG 209 215 DBREF 9PMG D 201 208 PDB 9PMG 9PMG 201 208 SEQRES 1 A 22 DG DG DA DT DG DC DC DT DG DT DA DC DG SEQRES 2 A 22 DG DA DC DA DG DA DT DC DT SEQRES 1 B 7 DC DC DG DT DA DC DA SEQRES 1 C 7 DG DG DC DA DT DC DC SEQRES 1 D 8 DA DG DA DT DC DT DG DT CRYST1 133.133 133.133 62.784 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 0.007511 0.004337 0.000000 0.00000 SCALE2 0.000000 0.008673 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015928 0.00000 MASTER 289 0 0 0 0 0 0 6 893 4 0 5 END