HEADER RNA 22-MAR-23 8ITS TITLE CRYSTAL STRUCTURE OF DUF-3268 K-JUNCTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (46-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: BACTERIUM; SOURCE 4 ORGANISM_TAXID: 1869227 KEYWDS K-JUNCTION, K-TURN, RNA MOTIF, RNA EXPDTA X-RAY DIFFRACTION AUTHOR M.LI,D.M.J.LILLEY,L.HUANG REVDAT 1 27-MAR-24 8ITS 0 JRNL AUTH M.LI,D.M.J.LILLEY,L.HUANG JRNL TITL CRYSTAL STRUCTURE OF DUF-3268 K-JUNCTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.94 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) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 8881 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 432 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 20.1900 - 2.8000 1.00 2975 151 0.1708 0.1773 REMARK 3 2 2.8000 - 2.2200 1.00 2893 171 0.2563 0.3024 REMARK 3 3 2.2200 - 1.9400 0.88 2581 110 0.2713 0.3245 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.646 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.63 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 : 0.001 1113 REMARK 3 ANGLE : 0.332 1735 REMARK 3 CHIRALITY : 0.014 230 REMARK 3 PLANARITY : 0.002 46 REMARK 3 DIHEDRAL : 10.885 549 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 41 THROUGH 45 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.1012 -33.9632 16.7498 REMARK 3 T TENSOR REMARK 3 T11: 0.2407 T22: 0.3063 REMARK 3 T33: 0.2894 T12: 0.0075 REMARK 3 T13: -0.0390 T23: 0.0110 REMARK 3 L TENSOR REMARK 3 L11: 1.4500 L22: 2.5080 REMARK 3 L33: 2.9470 L12: 0.3341 REMARK 3 L13: -0.0696 L23: -0.8935 REMARK 3 S TENSOR REMARK 3 S11: -0.0177 S12: -0.5231 S13: 0.0783 REMARK 3 S21: 0.3108 S22: -0.3939 S23: -0.8322 REMARK 3 S31: 0.0624 S32: 0.7748 S33: 0.3575 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 46 THROUGH 46 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.4873 -23.3277 12.5691 REMARK 3 T TENSOR REMARK 3 T11: 0.3794 T22: 0.5007 REMARK 3 T33: 0.4336 T12: -0.0928 REMARK 3 T13: -0.0056 T23: -0.0387 REMARK 3 L TENSOR REMARK 3 L11: 1.9420 L22: 0.2672 REMARK 3 L33: 3.0068 L12: 0.2866 REMARK 3 L13: 0.1127 L23: 0.7181 REMARK 3 S TENSOR REMARK 3 S11: 0.3551 S12: -0.3244 S13: -0.0573 REMARK 3 S21: 0.0371 S22: 0.0380 S23: -0.3575 REMARK 3 S31: -0.0805 S32: -0.1032 S33: -0.3759 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 20 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.4686 -28.4550 5.7251 REMARK 3 T TENSOR REMARK 3 T11: 0.2688 T22: 0.3050 REMARK 3 T33: 0.2944 T12: -0.0077 REMARK 3 T13: -0.0191 T23: 0.0069 REMARK 3 L TENSOR REMARK 3 L11: 0.4617 L22: 0.4413 REMARK 3 L33: 1.2580 L12: -0.1646 REMARK 3 L13: -0.2241 L23: 0.3189 REMARK 3 S TENSOR REMARK 3 S11: 0.0059 S12: -0.0339 S13: 0.0896 REMARK 3 S21: -0.0604 S22: -0.0043 S23: -0.0038 REMARK 3 S31: 0.0052 S32: 0.2557 S33: 0.0128 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 21 THROUGH 40 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.6094 -36.5283 18.9704 REMARK 3 T TENSOR REMARK 3 T11: 0.2691 T22: 0.2467 REMARK 3 T33: 0.3114 T12: -0.0023 REMARK 3 T13: -0.0021 T23: -0.0096 REMARK 3 L TENSOR REMARK 3 L11: 0.4496 L22: 0.2367 REMARK 3 L33: 1.2280 L12: -0.1637 REMARK 3 L13: 0.3751 L23: -0.5553 REMARK 3 S TENSOR REMARK 3 S11: 0.0242 S12: -0.0492 S13: 0.0056 REMARK 3 S21: -0.0173 S22: 0.0214 S23: 0.0730 REMARK 3 S31: 0.1313 S32: -0.0193 S33: -0.0453 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 8ITS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-APR-23. REMARK 100 THE DEPOSITION ID IS D_1300036356. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97851 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8884 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.940 REMARK 200 RESOLUTION RANGE LOW (A) : 20.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.12300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.72400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 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 (%): 44.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MAGNESIUM ACETATE, 30% V/V 2 REMARK 280 -METHYL-2,4-PENTANEDIOL, 0.5 M SODIUM FLUORIDE, PH 6.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 39.77000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.36500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 39.77000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.36500 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 9 OP1 REMARK 620 2 HOH A 212 O 102.4 REMARK 620 3 HOH A 221 O 83.8 106.4 REMARK 620 4 HOH A 232 O 73.3 163.2 89.4 REMARK 620 5 HOH A 258 O 160.7 96.5 95.0 87.4 REMARK 620 6 HOH A 307 O 89.2 83.1 169.2 80.7 88.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 229 O REMARK 620 2 HOH A 240 O 82.3 REMARK 620 3 HOH A 242 O 90.9 84.2 REMARK 620 4 HOH A 259 O 97.9 95.3 171.1 REMARK 620 5 HOH A 313 O 171.7 90.6 84.1 87.0 REMARK 620 6 HOH A 315 O 92.2 171.2 89.0 92.3 94.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 220 O REMARK 620 2 HOH A 249 O 103.0 REMARK 620 3 HOH A 266 O 97.1 159.4 REMARK 620 4 HOH A 269 O 92.6 89.0 94.7 REMARK 620 5 HOH A 276 O 98.8 83.5 89.0 167.5 REMARK 620 6 HOH A 317 O 174.6 76.3 84.1 82.0 86.5 REMARK 620 N 1 2 3 4 5 DBREF 8ITS A 1 46 PDB 8ITS 8ITS 1 46 SEQRES 1 A 46 G G G A G U U A G A C U C SEQRES 2 A 46 G C G A A A G C G A G G A SEQRES 3 A 46 A C U G C G A A A G C A G SEQRES 4 A 46 U A C U U C C HET MG A 101 1 HET MG A 102 1 HET MG A 103 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG 3(MG 2+) FORMUL 5 HOH *118(H2 O) LINK OP1 G A 9 MG MG A 103 1555 1555 2.41 LINK MG MG A 101 O HOH A 229 1555 1555 2.15 LINK MG MG A 101 O HOH A 240 1555 1555 2.03 LINK MG MG A 101 O HOH A 242 1555 1555 2.14 LINK MG MG A 101 O HOH A 259 1555 1555 2.12 LINK MG MG A 101 O HOH A 313 1555 1555 2.08 LINK MG MG A 101 O HOH A 315 1555 1555 2.08 LINK MG MG A 102 O HOH A 220 1555 1555 2.02 LINK MG MG A 102 O HOH A 249 1555 1555 2.05 LINK MG MG A 102 O HOH A 266 1555 1555 2.08 LINK MG MG A 102 O HOH A 269 1555 1555 2.08 LINK MG MG A 102 O HOH A 276 1555 1555 2.08 LINK MG MG A 102 O HOH A 317 1555 1555 2.08 LINK MG MG A 103 O HOH A 212 1555 1555 2.15 LINK MG MG A 103 O HOH A 221 1555 1555 2.21 LINK MG MG A 103 O HOH A 232 1555 1555 2.07 LINK MG MG A 103 O HOH A 258 1555 4556 2.17 LINK MG MG A 103 O HOH A 307 1555 1555 2.15 CRYST1 79.540 38.730 49.800 90.00 125.83 90.00 C 1 2 1 4 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 0.012572 0.000000 0.009077 0.00000 SCALE2 0.000000 0.025820 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024767 0.00000