HEADER RNA 16-JUL-24 9G4R TITLE CRYSTAL STRUCTURE OF THE DUF2693-FD RNA MOTIF COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (47-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: PHOCAEICOLA DOREI CL03T12C01; SOURCE 4 ORGANISM_TAXID: 997877 KEYWDS RNA STRUCTURE; TRNA-MIMICKING; X-RAY CRYSTALLOGRAPHY, RNA EXPDTA X-RAY DIFFRACTION AUTHOR L.HUANG,D.M.J.LILLEY REVDAT 1 30-JUL-25 9G4R 0 JRNL AUTH L.HUANG,D.M.J.LILLEY JRNL TITL STRUCTURAL BASIS FOR TRNA-MIMICKING BY DUF2693-FD RNA MOTIF JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 16698 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT : 901 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 47.9600 - 4.5955 1.00 2700 164 0.1327 0.1491 REMARK 3 2 4.5955 - 3.6480 1.00 2695 157 0.1524 0.2025 REMARK 3 3 3.6480 - 3.1869 1.00 2718 129 0.1913 0.2465 REMARK 3 4 3.1869 - 2.8956 0.98 2634 165 0.2635 0.2721 REMARK 3 5 2.8956 - 2.6881 0.96 2603 161 0.4300 0.4927 REMARK 3 6 2.6881 - 2.5300 0.90 2447 125 0.4385 0.4230 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.440 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 1145 REMARK 3 ANGLE : 1.256 1786 REMARK 3 CHIRALITY : 0.045 233 REMARK 3 PLANARITY : 0.008 47 REMARK 3 DIHEDRAL : 15.945 560 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 16 THROUGH 25 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.5908 52.2339 39.1773 REMARK 3 T TENSOR REMARK 3 T11: 0.6389 T22: 0.4577 REMARK 3 T33: 0.5838 T12: -0.0452 REMARK 3 T13: -0.0028 T23: 0.0220 REMARK 3 L TENSOR REMARK 3 L11: 6.2904 L22: 1.5199 REMARK 3 L33: 9.3279 L12: -2.7501 REMARK 3 L13: -2.9467 L23: 2.2924 REMARK 3 S TENSOR REMARK 3 S11: -0.0314 S12: -0.2647 S13: -0.5514 REMARK 3 S21: 0.1456 S22: -0.2370 S23: 0.0995 REMARK 3 S31: 1.0370 S32: 0.3264 S33: 0.3066 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 26 THROUGH 47 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.3398 46.9419 38.8465 REMARK 3 T TENSOR REMARK 3 T11: 0.6384 T22: 0.9418 REMARK 3 T33: 0.6393 T12: 0.1426 REMARK 3 T13: -0.0116 T23: 0.0973 REMARK 3 L TENSOR REMARK 3 L11: 6.2705 L22: 1.9666 REMARK 3 L33: 7.3126 L12: -2.5645 REMARK 3 L13: -5.0903 L23: 2.7020 REMARK 3 S TENSOR REMARK 3 S11: -0.3832 S12: -1.1821 S13: -0.1570 REMARK 3 S21: 0.3828 S22: 0.3575 S23: -0.2099 REMARK 3 S31: 1.0213 S32: 1.2407 S33: 0.0303 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.0574 50.4710 32.2213 REMARK 3 T TENSOR REMARK 3 T11: 0.5580 T22: 0.7609 REMARK 3 T33: 0.5206 T12: 0.1239 REMARK 3 T13: 0.0614 T23: 0.0960 REMARK 3 L TENSOR REMARK 3 L11: 6.7921 L22: 3.2207 REMARK 3 L33: 4.5962 L12: -2.9820 REMARK 3 L13: -4.0768 L23: 3.3827 REMARK 3 S TENSOR REMARK 3 S11: -0.1663 S12: -0.6088 S13: -0.2822 REMARK 3 S21: 0.2817 S22: 0.0917 S23: 0.0193 REMARK 3 S31: 0.7137 S32: 0.8454 S33: 0.1923 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 11 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.7271 65.6828 40.2337 REMARK 3 T TENSOR REMARK 3 T11: 0.8508 T22: 0.6700 REMARK 3 T33: 0.6428 T12: -0.0729 REMARK 3 T13: -0.0522 T23: -0.0344 REMARK 3 L TENSOR REMARK 3 L11: 8.8014 L22: 9.8102 REMARK 3 L33: 3.9674 L12: 5.1342 REMARK 3 L13: -0.5310 L23: -5.4876 REMARK 3 S TENSOR REMARK 3 S11: -0.3664 S12: 0.1815 S13: 0.8490 REMARK 3 S21: 0.4612 S22: -0.0353 S23: 0.7008 REMARK 3 S31: -1.8101 S32: 0.8738 S33: 0.2558 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 9G4R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-JUL-24. REMARK 100 THE DEPOSITION ID IS D_1292140337. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9159 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16698 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.530 REMARK 200 RESOLUTION RANGE LOW (A) : 47.961 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.800 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.80000 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: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM CHLORIDE 0.1M POTASSIUM REMARK 280 CHLORIDE 0.05M HEPES6.5 1.9M LITHIUM SULFATE, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 49.85600 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 24.92800 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 37.39200 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 12.46400 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 62.32000 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 49.85600 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 24.92800 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 12.46400 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 37.39200 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 62.32000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL 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 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 G A 11 O3' - P - OP1 ANGL. DEV. = 7.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 9G4R A 1 47 PDB 9G4R 9G4R 1 47 SEQRES 1 A 47 C C CBV U A C A G A C G G A SEQRES 2 A 47 U U G A A C G G C A A C C SEQRES 3 A 47 G A U A G C G A G A A U C SEQRES 4 A 47 G G G U A G G G HET CBV A 3 32 HET SO4 A 101 5 HET SO4 A 102 5 HET NA A 103 1 HETNAM CBV 5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM SO4 SULFATE ION HETNAM NA SODIUM ION FORMUL 1 CBV C9 H13 BR N3 O8 P FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 NA NA 1+ FORMUL 5 HOH *2(H2 O) LINK O3' C A 2 P CBV A 3 1555 1555 1.59 LINK O3' CBV A 3 P U A 4 1555 1555 1.60 CRYST1 110.761 110.761 74.784 90.00 90.00 120.00 P 65 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 0.009028 0.005213 0.000000 0.00000 SCALE2 0.000000 0.010425 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013372 0.00000 CONECT 26 38 CONECT 38 26 39 40 41 CONECT 39 38 CONECT 40 38 CONECT 41 38 42 CONECT 42 41 43 59 60 CONECT 43 42 44 45 61 CONECT 44 43 49 CONECT 45 43 46 47 62 CONECT 46 45 63 70 CONECT 47 45 48 49 64 CONECT 48 47 65 CONECT 49 44 47 50 66 CONECT 50 49 51 57 CONECT 51 50 52 53 CONECT 52 51 CONECT 53 51 54 CONECT 54 53 55 56 CONECT 55 54 67 68 CONECT 56 54 57 58 CONECT 57 50 56 69 CONECT 58 56 CONECT 59 42 CONECT 60 42 CONECT 61 43 CONECT 62 45 CONECT 63 46 CONECT 64 47 CONECT 65 48 CONECT 66 49 CONECT 67 55 CONECT 68 55 CONECT 69 57 CONECT 70 46 CONECT 1027 1028 1029 1030 1031 CONECT 1028 1027 CONECT 1029 1027 CONECT 1030 1027 CONECT 1031 1027 CONECT 1032 1033 1034 1035 1036 CONECT 1033 1032 CONECT 1034 1032 CONECT 1035 1032 CONECT 1036 1032 MASTER 309 0 4 0 0 0 0 6 1027 1 44 4 END