HEADER RNA 17-MAY-16 5G4T TITLE THE STRUCTURE OF A QUASI-CYCLIC SIX K-TURN DUPLEX RNA SPECIES COMPND MOL_ID: 1; COMPND 2 MOLECULE: HMKT-7; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINK TURN MOTIF; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HMKT-7; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: KINK TURN MOTIF; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HALOARCULA MARISMORTUI; SOURCE 4 ORGANISM_TAXID: 2238; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: HALOARCULA MARISMORTUI; SOURCE 8 ORGANISM_TAXID: 2238 KEYWDS RNA, KINK TURN, RNA MOTIF, NANO-STRUCTURE, NANOTECHNOLOGY EXPDTA X-RAY DIFFRACTION AUTHOR L.HUANG,D.M.J.LILLEY REVDAT 2 10-JAN-24 5G4T 1 JRNL REVDAT 1 28-SEP-16 5G4T 0 JRNL AUTH L.HUANG,D.M.J.LILLEY JRNL TITL A QUASI-CYCLIC RNA NANO-SCALE MOLECULAR OBJECT CONSTRUCTED JRNL TITL 2 USING KINK TURNS. JRNL REF NANOSCALE V. 8 15189 2016 JRNL REFN ISSN 2040-3364 JRNL PMID 27506301 JRNL DOI 10.1039/C6NR05186C REMARK 2 REMARK 2 RESOLUTION. 2.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 2019 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.800 REMARK 3 FREE R VALUE TEST SET COUNT : 118 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 37.6146 - 2.7509 0.99 1901 118 0.1948 0.2348 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.070 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 109.3 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 137.2 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 : 0.003 467 REMARK 3 ANGLE : 0.630 726 REMARK 3 CHIRALITY : 0.034 95 REMARK 3 PLANARITY : 0.005 19 REMARK 3 DIHEDRAL : 14.195 222 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 1:4) REMARK 3 ORIGIN FOR THE GROUP (A): 58.2103 5.0525 53.3685 REMARK 3 T TENSOR REMARK 3 T11: 1.7327 T22: 1.4389 REMARK 3 T33: 1.1109 T12: 0.0757 REMARK 3 T13: 0.0184 T23: -0.1510 REMARK 3 L TENSOR REMARK 3 L11: 5.7805 L22: 5.4694 REMARK 3 L33: 5.4591 L12: -5.7627 REMARK 3 L13: -5.6251 L23: 5.3021 REMARK 3 S TENSOR REMARK 3 S11: 1.0394 S12: -0.0490 S13: 0.4160 REMARK 3 S21: -0.4978 S22: 0.0101 S23: 0.1693 REMARK 3 S31: 2.3462 S32: 0.2142 S33: -1.2487 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 5:8) REMARK 3 ORIGIN FOR THE GROUP (A): 53.6610 16.5909 57.7986 REMARK 3 T TENSOR REMARK 3 T11: 1.9068 T22: 1.2728 REMARK 3 T33: 0.9889 T12: -0.0321 REMARK 3 T13: 0.0192 T23: -0.2216 REMARK 3 L TENSOR REMARK 3 L11: 3.2840 L22: 3.8015 REMARK 3 L33: 8.0804 L12: 1.9887 REMARK 3 L13: -2.6124 L23: 1.9512 REMARK 3 S TENSOR REMARK 3 S11: 0.1423 S12: -0.2883 S13: 1.5857 REMARK 3 S21: 1.5824 S22: -0.5680 S23: -0.2328 REMARK 3 S31: 1.0467 S32: 1.3860 S33: 0.3470 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 9:11) REMARK 3 ORIGIN FOR THE GROUP (A): 50.6214 19.9541 44.3500 REMARK 3 T TENSOR REMARK 3 T11: 1.5972 T22: 1.9016 REMARK 3 T33: 1.4051 T12: 0.0512 REMARK 3 T13: -0.0800 T23: 0.1641 REMARK 3 L TENSOR REMARK 3 L11: 2.3938 L22: 5.6040 REMARK 3 L33: 1.6009 L12: 2.4481 REMARK 3 L13: 0.1536 L23: -1.3648 REMARK 3 S TENSOR REMARK 3 S11: -1.3418 S12: 0.3873 S13: 2.0146 REMARK 3 S21: 0.4590 S22: 1.7022 S23: -0.0889 REMARK 3 S31: 1.6154 S32: -3.0877 S33: -0.6814 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN B AND RESID 12:16) REMARK 3 ORIGIN FOR THE GROUP (A): 48.3535 22.9605 52.6918 REMARK 3 T TENSOR REMARK 3 T11: 1.9531 T22: 1.4139 REMARK 3 T33: 1.5872 T12: 0.3269 REMARK 3 T13: 0.3408 T23: 0.2171 REMARK 3 L TENSOR REMARK 3 L11: 3.6985 L22: 4.8419 REMARK 3 L33: 6.5025 L12: 1.3752 REMARK 3 L13: -3.8600 L23: -4.6625 REMARK 3 S TENSOR REMARK 3 S11: 0.8568 S12: 0.0656 S13: 2.1682 REMARK 3 S21: 0.5606 S22: 1.3773 S23: 1.2411 REMARK 3 S31: -2.7157 S32: -2.5947 S33: -2.4974 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN B AND RESID 17:19) REMARK 3 ORIGIN FOR THE GROUP (A): 51.8334 8.3870 47.3584 REMARK 3 T TENSOR REMARK 3 T11: 1.8993 T22: 1.4826 REMARK 3 T33: 1.1764 T12: -0.0780 REMARK 3 T13: -0.2830 T23: -0.1859 REMARK 3 L TENSOR REMARK 3 L11: 5.0216 L22: 3.1865 REMARK 3 L33: 3.5533 L12: -3.8717 REMARK 3 L13: 3.5403 L23: -2.7378 REMARK 3 S TENSOR REMARK 3 S11: -0.1935 S12: -1.9695 S13: 1.0661 REMARK 3 S21: -1.5506 S22: -0.3485 S23: 1.3948 REMARK 3 S31: -0.2037 S32: -2.0676 S33: -0.6839 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 5G4T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1290066867. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.920 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PIXEL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2019 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 28.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.800 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.60 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.30 REMARK 200 R MERGE FOR SHELL (I) : 1.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.800 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 4CS1 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.5 M NA FORMATE, 0.1 M NA ACETATE (PH REMARK 280 4.6) REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 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 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 23.91350 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 23.91350 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 23.91350 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 23.91350 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 23.91350 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 23.91350 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 BIOMT1 2 0.500000 -0.866025 0.000000 35.15300 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 60.88678 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 119.56750 DBREF 5G4T A 1 11 PDB 5G4T 5G4T 1 11 DBREF 5G4T B 12 19 PDB 5G4T 5G4T 12 19 SEQRES 1 A 11 G G C G A A G A A C U SEQRES 1 B 8 G G G G A G C U CRYST1 70.306 70.306 47.827 90.00 90.00 120.00 P 63 2 2 12 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 0.014224 0.008212 0.000000 0.00000 SCALE2 0.000000 0.016424 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020909 0.00000