HEADER DNA 18-APR-23 8SJR TITLE [3T17] SELF-ASSEMBLING RIGHT-HANDED TENSEGRITY TRIANGLE WITH 17 TITLE 2 INTERJUNCTION BASE PAIRS AND R3 SYMMETRY COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*CP*AP*GP*CP*AP*GP*CP*CP*TP*GP*AP*AP*TP*AP*CP*CP*GP*CP*A)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'- COMPND 8 D(P*GP*CP*GP*GP*TP*AP*TP*TP*CP*AP*CP*CP*AP*CP*GP*AP*T)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*TP*GP*CP*GP*CP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3'); COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA (5'-D(P*TP*CP*GP*TP*GP*GP*AP*CP*AP*GP*CP*G)-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 TENSEGRITY TRIANGLE, DNA NANOTECHNOLOGY, NANOMATERIALS, DNA EXPDTA X-RAY DIFFRACTION AUTHOR J.JANOWSKI,S.VECCHIONI,R.SHA,Y.P.OHAYON REVDAT 2 08-MAY-24 8SJR 1 JRNL REVDAT 1 24-APR-24 8SJR 0 JRNL AUTH J.JANOWSKI,V.A.B.PHAM,S.VECCHIONI,K.WOLOSZYN,B.LU,Y.ZOU, JRNL AUTH 2 B.ERKALO,L.PERREN,J.RUEB,J.MADNICK,C.MAO,M.SAITO,Y.P.OHAYON, JRNL AUTH 3 N.JONOSKA,R.SHA JRNL TITL ENGINEERING TERTIARY CHIRALITY IN HELICAL BIOPOLYMERS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 121 92121 2024 JRNL REFN ESSN 1091-6490 JRNL PMID 38684000 JRNL DOI 10.1073/PNAS.2321992121 REMARK 2 REMARK 2 RESOLUTION. 5.25 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) : 5.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 55.9 REMARK 3 NUMBER OF REFLECTIONS : 3630 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.670 REMARK 3 FREE R VALUE TEST SET COUNT : 206 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 38.7200 - 5.2500 0.56 3424 206 0.2095 0.2501 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) : 48.714 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 412.2 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 407.8 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 : 0.009 1416 REMARK 3 ANGLE : 1.045 2177 REMARK 3 CHIRALITY : 0.056 246 REMARK 3 PLANARITY : 0.006 62 REMARK 3 DIHEDRAL : 40.824 606 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 101 THROUGH 119) REMARK 3 ORIGIN FOR THE GROUP (A): 31.5248 -8.6039 -5.2764 REMARK 3 T TENSOR REMARK 3 T11: 1.8186 T22: 5.4051 REMARK 3 T33: 4.9883 T12: -2.7574 REMARK 3 T13: -0.4684 T23: -4.9514 REMARK 3 L TENSOR REMARK 3 L11: 0.7980 L22: 5.6139 REMARK 3 L33: 5.2409 L12: -0.2752 REMARK 3 L13: -0.3402 L23: -5.1824 REMARK 3 S TENSOR REMARK 3 S11: 1.6692 S12: 0.7104 S13: -1.4359 REMARK 3 S21: -0.9934 S22: 0.2639 S23: -0.1057 REMARK 3 S31: 2.4294 S32: -0.7865 S33: 0.5348 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 98 THROUGH 114) REMARK 3 ORIGIN FOR THE GROUP (A): 21.9411 -2.1646 -11.1660 REMARK 3 T TENSOR REMARK 3 T11: 1.3740 T22: 5.7660 REMARK 3 T33: 6.5175 T12: -0.0298 REMARK 3 T13: 0.5886 T23: -3.2330 REMARK 3 L TENSOR REMARK 3 L11: 2.9345 L22: 7.1368 REMARK 3 L33: 7.3043 L12: 0.8393 REMARK 3 L13: 0.7192 L23: -2.1760 REMARK 3 S TENSOR REMARK 3 S11: 2.1422 S12: 0.5618 S13: 2.8758 REMARK 3 S21: 0.3199 S22: 1.6591 S23: -1.1557 REMARK 3 S31: -1.3181 S32: -2.5696 S33: -0.9834 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'C' AND RESID 101 THROUGH 114) REMARK 3 ORIGIN FOR THE GROUP (A): 42.9428 -0.3971 -12.9601 REMARK 3 T TENSOR REMARK 3 T11: 1.6332 T22: 3.2662 REMARK 3 T33: 6.4007 T12: 1.4770 REMARK 3 T13: -0.7839 T23: 1.1441 REMARK 3 L TENSOR REMARK 3 L11: 5.9775 L22: 8.1674 REMARK 3 L33: 4.2013 L12: 3.0319 REMARK 3 L13: 1.4077 L23: 2.2466 REMARK 3 S TENSOR REMARK 3 S11: 4.7837 S12: -0.7535 S13: -1.5747 REMARK 3 S21: -0.0335 S22: -0.9948 S23: -1.5889 REMARK 3 S31: 1.1657 S32: -1.0115 S33: -1.7072 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN 'D' AND RESID 110 THROUGH 121) REMARK 3 ORIGIN FOR THE GROUP (A): 32.7542 5.9730 -17.9677 REMARK 3 T TENSOR REMARK 3 T11: 2.9015 T22: 3.5621 REMARK 3 T33: 6.4432 T12: -0.0870 REMARK 3 T13: 3.2320 T23: -2.4146 REMARK 3 L TENSOR REMARK 3 L11: 0.5333 L22: 0.8769 REMARK 3 L33: 2.0900 L12: -0.5678 REMARK 3 L13: 0.2758 L23: 0.5298 REMARK 3 S TENSOR REMARK 3 S11: 1.2531 S12: 0.5319 S13: -0.2760 REMARK 3 S21: 0.1046 S22: 0.3815 S23: 0.9056 REMARK 3 S31: -1.5409 S32: 0.0076 S33: 3.1038 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 8SJR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-APR-23. REMARK 100 THE DEPOSITION ID IS D_1000273663. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAR-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 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) : 1.00744 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : STARANISO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3630 REMARK 200 RESOLUTION RANGE HIGH (A) : 5.250 REMARK 200 RESOLUTION RANGE LOW (A) : 85.107 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 81.0 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 5.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 6.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.90 REMARK 200 R MERGE FOR SHELL (I) : 6.16600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 15.10 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: PDB ENTRY 5W6W REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 89.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 11.7 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MOPS, 1.25 M MAGNESIUM SULFATE, REMARK 280 PH 7.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 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+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 85.10700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 49.13655 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.75067 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 85.10700 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 49.13655 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 26.75067 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 85.10700 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 49.13655 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 26.75067 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 98.27310 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 53.50133 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 98.27310 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 53.50133 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 98.27310 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 53.50133 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 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 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 0.00000 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 DG A 106 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA A 111 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA A 119 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DT C 101 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DA D 118 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 8SJR A 101 119 PDB 8SJR 8SJR 101 119 DBREF 8SJR B 98 114 PDB 8SJR 8SJR 98 114 DBREF 8SJR C 101 114 PDB 8SJR 8SJR 101 114 DBREF 8SJR D 110 121 PDB 8SJR 8SJR 110 121 SEQRES 1 A 19 DC DA DG DC DA DG DC DC DT DG DA DA DT SEQRES 2 A 19 DA DC DC DG DC DA SEQRES 1 B 17 DG DC DG DG DT DA DT DT DC DA DC DC DA SEQRES 2 B 17 DC DG DA DT SEQRES 1 C 14 DT DG DC DG DC DT DG DT DG DG DC DT DG SEQRES 2 C 14 DC SEQRES 1 D 12 DT DC DG DT DG DG DA DC DA DG DC DG CRYST1 170.214 170.214 80.252 90.00 90.00 120.00 H 3 9 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 0.005875 0.003392 0.000000 0.00000 SCALE2 0.000000 0.006784 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012461 0.00000