HEADER RNA 12-MAY-11 2YIE TITLE CRYSTAL STRUCTURE OF A F. NUCLEATUM FMN RIBOSWITCH BOUND TO FMN COMPND MOL_ID: 1; COMPND 2 MOLECULE: FMN RIBOSWITCH; COMPND 3 CHAIN: X; COMPND 4 FRAGMENT: APTAMER DOMAIN, RESIDUES 2495-2544; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: APTAMER DOMAIN BOUND TO FLAVIN MONONUCLEOTIDE; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: FMN RIBOSWITCH; COMPND 10 CHAIN: Z; COMPND 11 FRAGMENT: APTAMER DOMAIN, RESIDUES 2550-2601; COMPND 12 ENGINEERED: YES; COMPND 13 MUTATION: YES; COMPND 14 OTHER_DETAILS: APTAMER DOMAIN BOUND TO FLAVIN MONONUCLEOTIDE SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: FUSOBACTERIUM NUCLEATUM SUBSP. NUCLEATUM; SOURCE 4 ORGANISM_TAXID: 190304; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: FUSOBACTERIUM NUCLEATUM SUBSP. NUCLEATUM; SOURCE 8 ORGANISM_TAXID: 190304 KEYWDS RNA EXPDTA X-RAY DIFFRACTION AUTHOR Q.VICENS,E.MONDRAGON,R.T.BATEY REVDAT 3 20-DEC-23 2YIE 1 REMARK LINK REVDAT 2 09-NOV-11 2YIE 1 JRNL REVDAT 1 31-AUG-11 2YIE 0 JRNL AUTH Q.VICENS,E.MONDRAGON,R.T.BATEY JRNL TITL MOLECULAR SENSING BY THE APTAMER DOMAIN OF THE FMN JRNL TITL 2 RIBOSWITCH: A GENERAL MODEL FOR LIGAND BINDING BY JRNL TITL 3 CONFORMATIONAL SELECTION JRNL REF NUCLEIC ACIDS RES. V. 39 8586 2011 JRNL REFN ISSN 0305-1048 JRNL PMID 21745821 JRNL DOI 10.1093/NAR/GKR565 REMARK 2 REMARK 2 RESOLUTION. 2.94 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) : 2.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 9559 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 507 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 26.2933 - 4.2384 0.98 3127 179 0.1911 0.2162 REMARK 3 2 4.2384 - 3.3664 0.99 3006 163 0.2005 0.2204 REMARK 3 3 3.3664 - 2.9415 0.97 2919 165 0.2639 0.3216 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 : 0.83 REMARK 3 K_SOL : 0.25 REMARK 3 B_SOL : 43.74 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 80.36 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 96.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.62260 REMARK 3 B22 (A**2) : -6.62260 REMARK 3 B33 (A**2) : 13.24510 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 2730 REMARK 3 ANGLE : 0.612 4261 REMARK 3 CHIRALITY : 0.056 556 REMARK 3 PLANARITY : 0.005 112 REMARK 3 DIHEDRAL : 24.223 1379 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 12 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN Z AND RESID 57:61) REMARK 3 ORIGIN FOR THE GROUP (A): 6.8853 -62.8810 -58.7253 REMARK 3 T TENSOR REMARK 3 T11: 0.7305 T22: 2.3537 REMARK 3 T33: 1.5153 T12: -0.1247 REMARK 3 T13: 0.2952 T23: -0.3735 REMARK 3 L TENSOR REMARK 3 L11: 1.2494 L22: 8.3190 REMARK 3 L33: 0.2562 L12: 1.1174 REMARK 3 L13: -0.0151 L23: -1.4755 REMARK 3 S TENSOR REMARK 3 S11: 0.1555 S12: 1.9402 S13: 0.7914 REMARK 3 S21: -0.4400 S22: 0.3006 S23: 1.9285 REMARK 3 S31: 0.2890 S32: 2.2825 S33: -0.3170 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN Z AND RESID 62:66) REMARK 3 ORIGIN FOR THE GROUP (A): 27.3050 -58.9100 -71.5769 REMARK 3 T TENSOR REMARK 3 T11: 0.7719 T22: 0.7859 REMARK 3 T33: 0.5534 T12: -0.0698 REMARK 3 T13: -0.0554 T23: -0.0158 REMARK 3 L TENSOR REMARK 3 L11: 0.9540 L22: 0.8402 REMARK 3 L33: 0.8198 L12: 0.2247 REMARK 3 L13: 0.0632 L23: 0.2470 REMARK 3 S TENSOR REMARK 3 S11: -0.1855 S12: 0.2348 S13: -0.2243 REMARK 3 S21: -0.0193 S22: 0.2102 S23: 0.0048 REMARK 3 S31: 0.7215 S32: -0.3192 S33: -0.0660 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN Z AND RESID 67:78) REMARK 3 ORIGIN FOR THE GROUP (A): 28.9350 -44.7541 -80.8539 REMARK 3 T TENSOR REMARK 3 T11: 0.3626 T22: 0.3714 REMARK 3 T33: 0.4612 T12: -0.0585 REMARK 3 T13: 0.0799 T23: -0.1083 REMARK 3 L TENSOR REMARK 3 L11: 3.7990 L22: 1.2130 REMARK 3 L33: 2.5729 L12: 0.5282 REMARK 3 L13: -0.5077 L23: 1.0356 REMARK 3 S TENSOR REMARK 3 S11: 0.0650 S12: -0.7587 S13: 1.4197 REMARK 3 S21: -0.0356 S22: -0.1216 S23: 0.4950 REMARK 3 S31: -0.4135 S32: 0.2492 S33: 0.0035 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN Z AND RESID 79:98) REMARK 3 ORIGIN FOR THE GROUP (A): 18.5514 -76.1059 -75.6039 REMARK 3 T TENSOR REMARK 3 T11: 0.7615 T22: 0.6762 REMARK 3 T33: 0.6258 T12: -0.0036 REMARK 3 T13: 0.0274 T23: 0.0137 REMARK 3 L TENSOR REMARK 3 L11: 1.8644 L22: 1.2484 REMARK 3 L33: 0.9681 L12: -1.0002 REMARK 3 L13: -0.0341 L23: -1.2305 REMARK 3 S TENSOR REMARK 3 S11: 0.0874 S12: -0.0709 S13: 0.1701 REMARK 3 S21: -0.2482 S22: 0.0379 S23: 0.0502 REMARK 3 S31: 0.4192 S32: 0.1422 S33: -0.0150 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN Z AND RESID 99:106) REMARK 3 ORIGIN FOR THE GROUP (A): -0.6527 -65.4455 -77.1439 REMARK 3 T TENSOR REMARK 3 T11: 0.6922 T22: 1.0212 REMARK 3 T33: 1.3457 T12: 0.1598 REMARK 3 T13: -0.0214 T23: 0.0779 REMARK 3 L TENSOR REMARK 3 L11: 0.2093 L22: 1.8212 REMARK 3 L33: 0.7906 L12: 0.1547 REMARK 3 L13: 0.5002 L23: 0.4870 REMARK 3 S TENSOR REMARK 3 S11: 0.1665 S12: -0.2261 S13: -0.7776 REMARK 3 S21: -0.0700 S22: -0.3998 S23: 1.2533 REMARK 3 S31: 0.2250 S32: -0.9875 S33: 0.0273 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN Z AND RESID 107:113) REMARK 3 ORIGIN FOR THE GROUP (A): -13.1103 -46.4331 -81.9627 REMARK 3 T TENSOR REMARK 3 T11: 1.0770 T22: 0.6860 REMARK 3 T33: 1.3655 T12: 0.3964 REMARK 3 T13: -0.1189 T23: 0.0082 REMARK 3 L TENSOR REMARK 3 L11: 6.0776 L22: 5.3655 REMARK 3 L33: 2.1374 L12: 5.3235 REMARK 3 L13: 0.1629 L23: 1.3098 REMARK 3 S TENSOR REMARK 3 S11: 0.4044 S12: 0.0691 S13: 0.9332 REMARK 3 S21: 1.5368 S22: -1.1105 S23: 1.8959 REMARK 3 S31: 0.2776 S32: 0.7149 S33: -0.0845 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN X AND RESID 1:5) REMARK 3 ORIGIN FOR THE GROUP (A): -11.8801 -48.8534 -75.1036 REMARK 3 T TENSOR REMARK 3 T11: 2.4400 T22: 0.9625 REMARK 3 T33: 1.4851 T12: 0.2883 REMARK 3 T13: -0.1985 T23: 0.1294 REMARK 3 L TENSOR REMARK 3 L11: 1.9703 L22: 5.1377 REMARK 3 L33: 2.5708 L12: -2.8760 REMARK 3 L13: -1.3283 L23: 3.2657 REMARK 3 S TENSOR REMARK 3 S11: -1.1927 S12: 0.4362 S13: -0.1583 REMARK 3 S21: 1.2970 S22: -0.1910 S23: 1.3605 REMARK 3 S31: -0.1984 S32: 0.0959 S33: 0.6283 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN X AND RESID 6:9) REMARK 3 ORIGIN FOR THE GROUP (A): -5.4727 -61.0906 -84.3032 REMARK 3 T TENSOR REMARK 3 T11: 0.6266 T22: 1.2454 REMARK 3 T33: 1.2216 T12: 0.1358 REMARK 3 T13: -0.2954 T23: 0.1638 REMARK 3 L TENSOR REMARK 3 L11: 2.1932 L22: 2.2652 REMARK 3 L33: 0.1501 L12: 2.1280 REMARK 3 L13: 0.1882 L23: 0.0176 REMARK 3 S TENSOR REMARK 3 S11: 1.0522 S12: -0.6011 S13: -0.4799 REMARK 3 S21: 0.3017 S22: -0.6791 S23: -0.4102 REMARK 3 S31: 0.0693 S32: -0.1970 S33: -0.0614 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN X AND RESID 10:19) REMARK 3 ORIGIN FOR THE GROUP (A): 22.8874 -80.1053 -86.2377 REMARK 3 T TENSOR REMARK 3 T11: 0.7529 T22: 0.6518 REMARK 3 T33: 0.6160 T12: 0.1533 REMARK 3 T13: -0.0559 T23: -0.0081 REMARK 3 L TENSOR REMARK 3 L11: 0.5725 L22: 0.9294 REMARK 3 L33: 0.7896 L12: -0.2901 REMARK 3 L13: -0.2845 L23: 0.7536 REMARK 3 S TENSOR REMARK 3 S11: -0.1864 S12: -0.0300 S13: -0.0653 REMARK 3 S21: 0.3239 S22: 0.0377 S23: 0.0225 REMARK 3 S31: 0.5285 S32: 0.2747 S33: 0.0916 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN X AND RESID 20:32) REMARK 3 ORIGIN FOR THE GROUP (A): 24.9118 -80.7683 -82.2455 REMARK 3 T TENSOR REMARK 3 T11: 0.5135 T22: 0.4858 REMARK 3 T33: 0.4845 T12: 0.0952 REMARK 3 T13: -0.0819 T23: -0.0717 REMARK 3 L TENSOR REMARK 3 L11: 1.0551 L22: 0.3412 REMARK 3 L33: 0.4629 L12: -0.9415 REMARK 3 L13: 0.1443 L23: -0.0366 REMARK 3 S TENSOR REMARK 3 S11: -0.0313 S12: 0.3074 S13: 0.0762 REMARK 3 S21: 0.2494 S22: 0.2300 S23: 0.0142 REMARK 3 S31: -0.0162 S32: 0.0313 S33: -0.0542 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN X AND RESID 33:48) REMARK 3 ORIGIN FOR THE GROUP (A): 13.7694 -54.3297 -74.3904 REMARK 3 T TENSOR REMARK 3 T11: 0.6710 T22: 0.6637 REMARK 3 T33: 0.7000 T12: 0.0525 REMARK 3 T13: 0.0306 T23: 0.0037 REMARK 3 L TENSOR REMARK 3 L11: 1.8636 L22: 0.4078 REMARK 3 L33: 1.8002 L12: 0.4330 REMARK 3 L13: -1.4078 L23: 0.1618 REMARK 3 S TENSOR REMARK 3 S11: 0.0629 S12: -0.2022 S13: 0.0868 REMARK 3 S21: -0.0423 S22: 0.1609 S23: -0.0920 REMARK 3 S31: -0.4923 S32: 0.0467 S33: -0.1412 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: (CHAIN X AND RESID 49:54) REMARK 3 ORIGIN FOR THE GROUP (A): 2.0883 -70.7748 -57.4857 REMARK 3 T TENSOR REMARK 3 T11: 0.5309 T22: 1.3553 REMARK 3 T33: 0.6860 T12: -0.0750 REMARK 3 T13: 0.3220 T23: 0.2745 REMARK 3 L TENSOR REMARK 3 L11: 3.1116 L22: 0.6152 REMARK 3 L33: 1.6284 L12: 0.6692 REMARK 3 L13: -2.2274 L23: -0.3502 REMARK 3 S TENSOR REMARK 3 S11: 0.6390 S12: -1.4264 S13: -0.6753 REMARK 3 S21: 0.1715 S22: 0.4721 S23: 0.4956 REMARK 3 S31: -0.2259 S32: -0.9746 S33: 0.4400 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE GAMMA PHOSPHATE OF GTP IS REMARK 3 DISORDERED ON CHAINS X AND Z REMARK 4 REMARK 4 2YIE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1290048274. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-AUG-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17834 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.950 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.48000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 3F2Q REMARK 200 REMARK 200 REMARK: DATA WAS COLLECTED BY ANNIE HEROUX AS PART OF THE REMARK 200 MACROMOLECULAR CRYSTALLOGRAPHY RESEARCH RESOURCE AT BROOKHAVEN REMARK 200 NSLS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RNA WAS CRYSTALLIZED FROM 15% PEG REMARK 280 -MONOMETHYL 550 ETHER, 0.1 M MGCL2, 0.05 M NA-HEPES PH 7.0, 1 MM REMARK 280 FMN REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 46.41700 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 92.83400 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 92.83400 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 46.41700 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9541 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16104 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -87.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: X, Z 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN X, A 2542 TO U REMARK 400 ENGINEERED RESIDUE IN CHAIN X, G 2543 TO C REMARK 400 ENGINEERED RESIDUE IN CHAIN X, U 2544 TO C REMARK 400 ENGINEERED RESIDUE IN CHAIN Z, C 2550 TO G REMARK 400 ENGINEERED RESIDUE IN CHAIN Z, U 2551 TO A REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GTP X 1 PG O1G O2G O3G REMARK 470 GTP Z 57 PG O1G O2G O3G 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 X1059 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A X 14 OP2 REMARK 620 2 HOH X2021 O 95.0 REMARK 620 3 HOH X2022 O 84.7 179.7 REMARK 620 4 HOH X2023 O 173.5 90.4 89.9 REMARK 620 5 HOH X2024 O 94.2 88.6 91.5 89.6 REMARK 620 6 HOH X2025 O 85.5 91.5 88.5 90.6 179.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG X1055 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G X 33 N7 REMARK 620 2 HOH X2011 O 84.5 REMARK 620 3 HOH X2012 O 94.4 177.4 REMARK 620 4 HOH X2013 O 166.7 91.2 90.4 REMARK 620 5 HOH X2014 O 76.8 90.2 91.9 90.6 REMARK 620 6 FMN Z1114 O2P 99.4 83.1 94.8 92.5 172.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG X1060 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH X2002 O REMARK 620 2 HOH X2003 O 111.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG Z1116 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U Z 89 O4 REMARK 620 2 A Z 92 OP2 89.8 REMARK 620 3 HOH Z2011 O 78.4 93.1 REMARK 620 4 HOH Z2012 O 100.8 84.5 177.5 REMARK 620 5 HOH Z2013 O 90.9 173.9 93.0 89.4 REMARK 620 6 HOH Z2014 O 167.9 88.9 89.7 91.0 91.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG Z1117 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C Z 95 OP1 REMARK 620 2 HOH Z2021 O 102.9 REMARK 620 3 HOH Z2022 O 76.9 179.8 REMARK 620 4 HOH Z2023 O 165.8 90.1 90.1 REMARK 620 5 HOH Z2024 O 95.6 89.0 91.0 90.3 REMARK 620 6 HOH Z2025 O 84.3 91.1 88.9 89.7 179.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN Z 1114 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG X 1060 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG Z 1115 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG Z 1116 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG X 1055 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG X 1061 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG Z 1117 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG Z 1118 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG X 1056 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG X 1058 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG X 1059 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG Z 1119 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2YIF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A F. NUCLEATUM FMN RIBOSWITCH - FREE STATE DBREF 2YIE X 3 52 GB 20095250 AE009951 2495 2544 DBREF 2YIE Z 58 109 GB 20095250 AE009951 2550 2601 SEQADV 2YIE GTP X 1 GB 20095250 EXPRESSION TAG SEQADV 2YIE G X 2 GB 20095250 EXPRESSION TAG SEQADV 2YIE U X 50 GB 20095250 A 2542 ENGINEERED MUTATION SEQADV 2YIE C X 51 GB 20095250 G 2543 ENGINEERED MUTATION SEQADV 2YIE C X 52 GB 20095250 U 2544 ENGINEERED MUTATION SEQADV 2YIE A X 53 GB 20095250 EXPRESSION TAG SEQADV 2YIE U X 54 GB 20095250 EXPRESSION TAG SEQADV 2YIE GTP Z 57 GB 20095250 EXPRESSION TAG SEQADV 2YIE G Z 58 GB 20095250 C 2550 ENGINEERED MUTATION SEQADV 2YIE A Z 59 GB 20095250 U 2551 ENGINEERED MUTATION SEQADV 2YIE U Z 110 GB 20095250 EXPRESSION TAG SEQADV 2YIE U Z 111 GB 20095250 EXPRESSION TAG SEQADV 2YIE C Z 112 GB 20095250 EXPRESSION TAG SEQADV 2YIE G Z 113 GB 20095250 EXPRESSION TAG SEQRES 1 X 54 GTP G A U C U U C G G G G C SEQRES 2 X 54 A G G G U G A A A U U C C SEQRES 3 X 54 C G A C C G G U G G U A U SEQRES 4 X 54 A G U C C A C G A A U C C SEQRES 5 X 54 A U SEQRES 1 Z 57 GTP G A U U G A U U U G G U SEQRES 2 Z 57 G A A A U U C C A A A A C SEQRES 3 Z 57 C G A C A G U A G A G U C SEQRES 4 Z 57 U G G A U G A G A G A A G SEQRES 5 Z 57 A U U C G MODRES 2YIE GTP X 1 G GUANOSINE-5'-TRIPHOSPHATE MODRES 2YIE GTP Z 57 G GUANOSINE-5'-TRIPHOSPHATE HET GTP X 1 28 HET GTP Z 57 28 HET MG X1055 1 HET MG X1056 1 HET MG X1057 1 HET MG X1058 1 HET MG X1059 1 HET MG X1060 1 HET MG X1061 1 HET MG X1062 1 HET K X1063 1 HET FMN Z1114 31 HET MG Z1115 1 HET MG Z1116 1 HET MG Z1117 1 HET MG Z1118 1 HET MG Z1119 1 HET MG Z1120 1 HET K Z1121 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION HETNAM FMN FLAVIN MONONUCLEOTIDE HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 1 GTP 2(C10 H16 N5 O14 P3) FORMUL 3 MG 14(MG 2+) FORMUL 11 K 2(K 1+) FORMUL 12 FMN C17 H21 N4 O9 P FORMUL 20 HOH *29(H2 O) LINK O3' GTP X 1 P G X 2 1555 1555 1.61 LINK O3' GTP Z 57 P G Z 58 1555 1555 1.61 LINK OP2 A X 14 MG MG X1059 1555 1555 2.20 LINK OP2 U X 23 MG MG X1058 1555 1555 2.80 LINK N7 G X 33 MG MG X1055 1555 1555 2.55 LINK MG MG X1055 O HOH X2011 1555 1555 1.85 LINK MG MG X1055 O HOH X2012 1555 1555 1.85 LINK MG MG X1055 O HOH X2013 1555 1555 1.89 LINK MG MG X1055 O HOH X2014 1555 1555 1.87 LINK MG MG X1055 O2P FMN Z1114 1555 1555 2.42 LINK MG MG X1056 O HOH X2005 1555 1555 2.79 LINK MG MG X1059 O HOH X2021 1555 1555 1.85 LINK MG MG X1059 O HOH X2022 1555 1555 1.85 LINK MG MG X1059 O HOH X2023 1555 1555 1.85 LINK MG MG X1059 O HOH X2024 1555 1555 1.85 LINK MG MG X1059 O HOH X2025 1555 1555 1.84 LINK MG MG X1060 O HOH X2002 1555 1555 2.81 LINK MG MG X1060 O HOH X2003 1555 1555 2.69 LINK O4 U Z 89 MG MG Z1116 1555 1555 2.54 LINK OP2 A Z 92 MG MG Z1116 1555 1555 2.33 LINK OP1 C Z 95 MG MG Z1117 1555 1555 2.45 LINK MG MG Z1116 O HOH Z2011 1555 1555 1.85 LINK MG MG Z1116 O HOH Z2012 1555 1555 1.85 LINK MG MG Z1116 O HOH Z2013 1555 1555 1.89 LINK MG MG Z1116 O HOH Z2014 1555 1555 1.87 LINK MG MG Z1117 O HOH Z2021 1555 1555 1.85 LINK MG MG Z1117 O HOH Z2022 1555 1555 1.84 LINK MG MG Z1117 O HOH Z2023 1555 1555 1.85 LINK MG MG Z1117 O HOH Z2024 1555 1555 1.85 LINK MG MG Z1117 O HOH Z2025 1555 1555 1.84 LINK MG MG Z1118 O HOH Z2003 1555 1555 2.60 SITE 1 AC1 14 G X 10 G X 11 G X 32 A X 48 SITE 2 AC1 14 A X 49 MG X1055 HOH X2011 HOH X2013 SITE 3 AC1 14 U Z 61 G Z 62 G Z 84 A Z 85 SITE 4 AC1 14 G Z 98 A Z 99 SITE 1 AC2 2 HOH X2002 HOH X2003 SITE 1 AC3 1 G Z 93 SITE 1 AC4 6 U Z 89 A Z 92 HOH Z2011 HOH Z2012 SITE 2 AC4 6 HOH Z2013 HOH Z2014 SITE 1 AC5 6 G X 33 HOH X2011 HOH X2012 HOH X2013 SITE 2 AC5 6 HOH X2014 FMN Z1114 SITE 1 AC6 1 U X 54 SITE 1 AC7 6 C Z 95 HOH Z2021 HOH Z2022 HOH Z2023 SITE 2 AC7 6 HOH Z2024 HOH Z2025 SITE 1 AC8 2 G Z 68 HOH Z2003 SITE 1 AC9 3 C X 13 G X 28 HOH X2005 SITE 1 BC1 2 A X 22 U X 23 SITE 1 BC2 6 A X 14 HOH X2021 HOH X2022 HOH X2023 SITE 2 BC2 6 HOH X2024 HOH X2025 SITE 1 BC3 2 A Z 90 G Z 91 CRYST1 73.679 73.679 139.251 90.00 90.00 120.00 P 31 2 1 6 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 0.013572 0.007836 0.000000 0.00000 SCALE2 0.000000 0.015672 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007181 0.00000 HETATM 1 O3B GTP X 1 -4.947 -42.567 -80.082 1.00186.34 O ANISOU 1 O3B GTP X 1 31592 18552 20655 1326 -6155 3376 O HETATM 2 PB GTP X 1 -4.338 -43.343 -78.884 1.00190.84 P ANISOU 2 PB GTP X 1 32295 19103 21114 1469 -5902 3323 P HETATM 3 O1B GTP X 1 -4.589 -44.819 -79.052 1.00183.67 O ANISOU 3 O1B GTP X 1 31197 18364 20227 1557 -5438 3196 O HETATM 4 O2B GTP X 1 -2.863 -43.089 -78.826 1.00204.45 O ANISOU 4 O2B GTP X 1 34048 20972 22662 1291 -6137 3512 O HETATM 5 O3A GTP X 1 -5.029 -42.819 -77.494 1.00187.36 O ANISOU 5 O3A GTP X 1 32185 18276 20729 1749 -5875 3166 O HETATM 6 PA GTP X 1 -4.861 -43.602 -76.154 1.00198.35 P ANISOU 6 PA GTP X 1 33821 19543 21999 2038 -5542 3052 P HETATM 7 O1A GTP X 1 -3.607 -44.465 -76.197 1.00204.88 O ANISOU 7 O1A GTP X 1 34584 20648 22612 1987 -5468 3152 O HETATM 8 O2A GTP X 1 -6.045 -44.465 -75.937 1.00182.23 O ANISOU 8 O2A GTP X 1 31749 17367 20122 2234 -5036 2831 O HETATM 9 O5' GTP X 1 -4.748 -42.531 -74.963 1.00200.44 O ANISOU 9 O5' GTP X 1 34375 19559 22224 2182 -5770 2993 O HETATM 10 C5' GTP X 1 -4.750 -42.937 -73.682 1.00203.35 C ANISOU 10 C5' GTP X 1 35018 19773 22472 2496 -5517 2862 C HETATM 11 C4' GTP X 1 -5.786 -42.377 -72.806 1.00195.51 C ANISOU 11 C4' GTP X 1 34258 18445 21584 2722 -5425 2702 C HETATM 12 O4' GTP X 1 -6.356 -41.247 -73.414 1.00184.63 O ANISOU 12 O4' GTP X 1 32745 17001 20403 2532 -5752 2713 O HETATM 13 C3' GTP X 1 -6.909 -43.328 -72.671 1.00183.08 C ANISOU 13 C3' GTP X 1 32825 16625 20113 2946 -4927 2604 C HETATM 14 O3' GTP X 1 -6.666 -44.266 -71.663 1.00191.95 O ANISOU 14 O3' GTP X 1 34240 17655 21036 3253 -4501 2546 O HETATM 15 C2' GTP X 1 -7.978 -42.487 -72.326 1.00174.76 C ANISOU 15 C2' GTP X 1 31874 15275 19252 3036 -4985 2475 C HETATM 16 O2' GTP X 1 -7.901 -42.168 -70.986 1.00184.50 O ANISOU 16 O2' GTP X 1 33376 16371 20355 3277 -4884 2361 O HETATM 17 C1' GTP X 1 -7.725 -41.268 -73.152 1.00171.53 C ANISOU 17 C1' GTP X 1 31229 15024 18919 2733 -5541 2572 C HETATM 18 N9 GTP X 1 -8.459 -41.301 -74.433 1.00150.51 N ANISOU 18 N9 GTP X 1 28270 12440 16477 2559 -5589 2556 N HETATM 19 C8 GTP X 1 -7.946 -41.273 -75.679 1.00148.31 C ANISOU 19 C8 GTP X 1 27713 12456 16180 2284 -5818 2708 C HETATM 20 N7 GTP X 1 -8.955 -41.371 -76.569 1.00138.75 N ANISOU 20 N7 GTP X 1 26239 11285 15195 2249 -5752 2557 N HETATM 21 C5 GTP X 1 -10.122 -41.467 -75.888 1.00135.01 C ANISOU 21 C5 GTP X 1 25827 10539 14930 2475 -5468 2281 C HETATM 22 C6 GTP X 1 -11.466 -41.589 -76.262 1.00130.08 C ANISOU 22 C6 GTP X 1 24980 9821 14625 2562 -5295 1969 C HETATM 23 O6 GTP X 1 -11.824 -41.639 -77.598 1.00130.07 O ANISOU 23 O6 GTP X 1 24633 10043 14745 2447 -5459 1897 O HETATM 24 N1 GTP X 1 -12.409 -41.662 -75.298 1.00131.16 N ANISOU 24 N1 GTP X 1 25244 9640 14953 2784 -4963 1711 N HETATM 25 C2 GTP X 1 -12.071 -41.620 -73.993 1.00132.57 C ANISOU 25 C2 GTP X 1 25810 9592 14969 2950 -4800 1782 C HETATM 26 N2 GTP X 1 -13.074 -41.685 -73.012 1.00132.92 N ANISOU 26 N2 GTP X 1 26016 9284 15202 3190 -4410 1522 N HETATM 27 N3 GTP X 1 -10.794 -41.506 -73.611 1.00138.61 N ANISOU 27 N3 GTP X 1 26811 10457 15398 2912 -5004 2069 N HETATM 28 C4 GTP X 1 -9.802 -41.428 -74.525 1.00140.39 C ANISOU 28 C4 GTP X 1 26875 10999 15469 2664 -5337 2305 C