HEADER DNA 04-JAN-26 9ZXK TITLE [A3T17] ASYMMETRIC THREE TURN TENSEGRITY TRIANGLE WITH PSUEDOSYMMETRY COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (31-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*TP*GP*TP*GP*AP*TP*GP*TP*GP*GP*TP*AP*GP*G)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (31-MER); COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: DNA (5'-D(*TP*TP*CP*GP*TP*AP*GP*TP*GP*GP*TP*CP*GP*C)-3'); COMPND 15 CHAIN: D; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 5; COMPND 18 MOLECULE: DNA (31-MER); COMPND 19 CHAIN: E; COMPND 20 ENGINEERED: YES; COMPND 21 MOL_ID: 6; COMPND 22 MOLECULE: DNA (5'-D(*TP*CP*AP*GP*TP*CP*GP*TP*GP*GP*TP*AP*TP*C)-3'); COMPND 23 CHAIN: F; COMPND 24 ENGINEERED: YES; COMPND 25 MOL_ID: 7; COMPND 26 MOLECULE: DNA (51-MER); COMPND 27 CHAIN: G; COMPND 28 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; SOURCE 17 MOL_ID: 5; SOURCE 18 SYNTHETIC: YES; SOURCE 19 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 20 ORGANISM_TAXID: 32630; SOURCE 21 MOL_ID: 6; SOURCE 22 SYNTHETIC: YES; SOURCE 23 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 24 ORGANISM_TAXID: 32630; SOURCE 25 MOL_ID: 7; SOURCE 26 SYNTHETIC: YES; SOURCE 27 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 28 ORGANISM_TAXID: 32630 KEYWDS TENSEGRITY TRIANGLE, DNA EXPDTA X-RAY DIFFRACTION AUTHOR S.VECCHIONI,K.WOLOSZYN,R.SHA,Y.P.OHAYON REVDAT 1 25-FEB-26 9ZXK 0 JRNL AUTH S.VECCHIONI,K.WOLOSZYN,R.SHA,Y.P.OHAYON,L.PERREN JRNL TITL SHAPE ANISOTROPY IN 3D DNA ARCHITECTURES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 5.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 5.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.980 REMARK 3 COMPLETENESS FOR RANGE (%) : 53.9 REMARK 3 NUMBER OF REFLECTIONS : 3797 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.710 REMARK 3 FREE R VALUE TEST SET COUNT : 141 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 45.4000 - 5.9600 0.54 3656 141 0.1493 0.1830 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) : 0.962 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.701 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 173.8 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 230.3 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 : 0.010 4250 REMARK 3 ANGLE : 1.029 6547 REMARK 3 CHIRALITY : 0.057 737 REMARK 3 PLANARITY : 0.006 186 REMARK 3 DIHEDRAL : 37.702 1832 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 1.0034 1.6533 -0.2340 REMARK 3 T TENSOR REMARK 3 T11: 1.9886 T22: 2.0523 REMARK 3 T33: 1.7492 T12: 0.3488 REMARK 3 T13: 0.1731 T23: 0.0745 REMARK 3 L TENSOR REMARK 3 L11: 0.9889 L22: 0.3395 REMARK 3 L33: 0.0851 L12: 0.7470 REMARK 3 L13: -0.4705 L23: -0.6422 REMARK 3 S TENSOR REMARK 3 S11: -0.8719 S12: -0.1325 S13: -0.4546 REMARK 3 S21: -0.1679 S22: 0.2223 S23: -0.0518 REMARK 3 S31: -0.6689 S32: 0.3837 S33: 0.3592 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 9ZXK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JAN-26. REMARK 100 THE DEPOSITION ID IS D_1000303910. 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 : 8.0 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 : 3825 REMARK 200 RESOLUTION RANGE HIGH (A) : 5.959 REMARK 200 RESOLUTION RANGE LOW (A) : 84.407 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.6 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 5.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 6.81 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 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 PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 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 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: HEPTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEPTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G 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 DT B 1 C5 DT B 1 C6 -0.045 REMARK 500 DT B 1 C4 DT B 1 O4 -0.056 REMARK 500 DT E 9 O3' DT E 9 C3' -0.042 REMARK 500 DC G 28 O3' DC G 28 C3' -0.045 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 DT A 12 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA A 14 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DC A 27 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC A 30 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT B 1 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DT B 1 C5 - C4 - O4 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT B 3 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG B 4 C3' - C2' - C1' ANGL. DEV. = -5.9 DEGREES REMARK 500 DG B 13 O4' - C4' - C3' ANGL. DEV. = -2.8 DEGREES REMARK 500 DG B 14 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG D 7 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC E 23 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT F 5 C3' - C2' - C1' ANGL. DEV. = -5.1 DEGREES REMARK 500 DT F 5 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT G 37 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DT G 42 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC G 46 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 9ZXK A 1 31 PDB 9ZXK 9ZXK 1 31 DBREF 9ZXK B 1 14 PDB 9ZXK 9ZXK 1 14 DBREF 9ZXK C 1 31 PDB 9ZXK 9ZXK 1 31 DBREF 9ZXK D 1 14 PDB 9ZXK 9ZXK 1 14 DBREF 9ZXK E 1 31 PDB 9ZXK 9ZXK 1 31 DBREF 9ZXK F 1 14 PDB 9ZXK 9ZXK 1 14 DBREF 9ZXK G 1 51 PDB 9ZXK 9ZXK 1 51 SEQRES 1 A 31 DG DA DC DC DT DA DC DC DT DG DG DT DG SEQRES 2 A 31 DA DG DT DA DC DG DT DT DC DA DG DG DA SEQRES 3 A 31 DC DG DA DC DT SEQRES 1 B 14 DT DG DT DG DA DT DG DT DG DG DT DA DG SEQRES 2 B 14 DG SEQRES 1 C 31 DC DA DG DC DG DA DC DC DT DG DC DT DC SEQRES 2 C 31 DT DC DG DT DC DT DT DG DT DC DG DG DA SEQRES 3 C 31 DC DA DT DC DA SEQRES 1 D 14 DT DT DC DG DT DA DG DT DG DG DT DC DG SEQRES 2 D 14 DC SEQRES 1 E 31 DA DA DG DA DT DA DC DC DT DG DA DT DA SEQRES 2 E 31 DA DT DA DG DG DT DT DG DA DC DG DG DA SEQRES 3 E 31 DC DT DA DC DG SEQRES 1 F 14 DT DC DA DG DT DC DG DT DG DG DT DA DT SEQRES 2 F 14 DC SEQRES 1 G 51 DG DT DA DC DT DC DA DC DC DA DC DC DG SEQRES 2 G 51 DA DC DA DA DG DA DC DG DA DG DA DG DC SEQRES 3 G 51 DA DC DC DG DT DC DA DA DC DC DT DA DT SEQRES 4 G 51 DT DA DT DC DA DC DC DT DG DA DA DC CRYST1 89.460 100.603 100.888 113.13 110.06 102.64 P 1 1 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 0.011178 0.002507 0.006235 0.00000 SCALE2 0.000000 0.010187 0.006047 0.00000 SCALE3 0.000000 0.000000 0.012271 0.00000 MASTER 252 0 0 0 0 0 0 6 3792 7 0 19 END