HEADER TRANSFERASE/RNA 16-MAY-13 4KR6 TITLE CRYSTAL STRUCTURE OF A 4-THIOURIDINE SYNTHETASE - RNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE TRNA SULFURTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SULFUR CARRIER PROTEIN THIS SULFURTRANSFERASE, THIAMINE COMPND 5 BIOSYNTHESIS PROTEIN THII, TRNA 4-THIOURIDINE SYNTHASE; COMPND 6 EC: 2.8.1.4; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: RNA (39-MER); COMPND 11 CHAIN: C, D; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 243274; SOURCE 4 STRAIN: ATCC 43589; SOURCE 5 GENE: AAD36761, THII, TM_1694; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS TRNA MODIFICATION, THIOURIDINE, SULFURTRANSFERASE, ADENYLATION, THUMP KEYWDS 2 DOMAIN, PP-LOOP MOTIF, 4-THIOURIDINE SYNTHESIS, TRANSFERASE-RNA KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.NEUMANN,R.FICNER,K.LAKOMEK REVDAT 4 20-SEP-23 4KR6 1 REMARK SEQADV REVDAT 3 04-SEP-19 4KR6 1 REMARK REVDAT 2 16-JUL-14 4KR6 1 JRNL REVDAT 1 23-APR-14 4KR6 0 JRNL AUTH P.NEUMANN,K.LAKOMEK,P.T.NAUMANN,W.M.ERWIN,C.T.LAUHON, JRNL AUTH 2 R.FICNER JRNL TITL CRYSTAL STRUCTURE OF A 4-THIOURIDINE SYNTHETASE-RNA COMPLEX JRNL TITL 2 REVEALS SPECIFICITY OF TRNA U8 MODIFICATION. JRNL REF NUCLEIC ACIDS RES. V. 42 6673 2014 JRNL REFN ISSN 0305-1048 JRNL PMID 24705700 JRNL DOI 10.1093/NAR/GKU249 REMARK 2 REMARK 2 RESOLUTION. 2.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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) : 2.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 30363 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1513 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 37.1815 - 6.3289 0.96 2785 146 0.1937 0.2385 REMARK 3 2 6.3289 - 5.0274 0.98 2698 142 0.1806 0.2415 REMARK 3 3 5.0274 - 4.3930 0.98 2699 143 0.1486 0.1794 REMARK 3 4 4.3930 - 3.9919 0.98 2693 140 0.1513 0.1767 REMARK 3 5 3.9919 - 3.7060 0.98 2675 141 0.1668 0.2027 REMARK 3 6 3.7060 - 3.4877 0.98 2677 141 0.1793 0.2473 REMARK 3 7 3.4877 - 3.3132 0.99 2659 138 0.2046 0.2243 REMARK 3 8 3.3132 - 3.1690 0.99 2700 143 0.2148 0.2790 REMARK 3 9 3.1690 - 3.0471 0.99 2647 140 0.2314 0.2984 REMARK 3 10 3.0471 - 2.9420 0.96 2593 140 0.2660 0.2797 REMARK 3 11 2.9420 - 2.8500 0.75 2024 99 0.2736 0.3153 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.70 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 60.02 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 83.33 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 : 0.012 8212 REMARK 3 ANGLE : 0.927 11453 REMARK 3 CHIRALITY : 0.062 1346 REMARK 3 PLANARITY : 0.004 1168 REMARK 3 DIHEDRAL : 16.917 3374 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND RESID 77:162 REMARK 3 ORIGIN FOR THE GROUP (A): 1.4744 21.1890 -13.2230 REMARK 3 T TENSOR REMARK 3 T11: 0.3534 T22: 0.5006 REMARK 3 T33: 0.3805 T12: 0.0992 REMARK 3 T13: 0.0286 T23: 0.0463 REMARK 3 L TENSOR REMARK 3 L11: 3.2494 L22: 3.6274 REMARK 3 L33: 3.2356 L12: -1.5548 REMARK 3 L13: -0.0410 L23: 0.8928 REMARK 3 S TENSOR REMARK 3 S11: -0.1325 S12: -0.3547 S13: -0.1998 REMARK 3 S21: 0.3198 S22: 0.2231 S23: 0.5025 REMARK 3 S31: 0.0286 S32: -0.4726 S33: 0.0966 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 1:76 REMARK 3 ORIGIN FOR THE GROUP (A): 15.3861 6.6487 -11.7529 REMARK 3 T TENSOR REMARK 3 T11: 0.3999 T22: 0.4075 REMARK 3 T33: 0.3685 T12: 0.0475 REMARK 3 T13: -0.0538 T23: -0.0024 REMARK 3 L TENSOR REMARK 3 L11: 2.1924 L22: 2.6576 REMARK 3 L33: 3.1214 L12: -0.1930 REMARK 3 L13: 1.0735 L23: -0.8037 REMARK 3 S TENSOR REMARK 3 S11: 0.0073 S12: 0.1873 S13: 0.0903 REMARK 3 S21: -0.0684 S22: -0.1461 S23: -0.0598 REMARK 3 S31: 0.1090 S32: 0.3659 S33: 0.1439 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 163:388 REMARK 3 ORIGIN FOR THE GROUP (A): 22.0402 -14.5153 15.0414 REMARK 3 T TENSOR REMARK 3 T11: 0.1986 T22: 0.2497 REMARK 3 T33: 0.3155 T12: -0.0303 REMARK 3 T13: -0.0006 T23: 0.0029 REMARK 3 L TENSOR REMARK 3 L11: 1.3522 L22: 2.1259 REMARK 3 L33: 2.1487 L12: -0.2738 REMARK 3 L13: 0.4383 L23: -0.7067 REMARK 3 S TENSOR REMARK 3 S11: -0.0000 S12: -0.0235 S13: -0.2660 REMARK 3 S21: -0.0797 S22: 0.0245 S23: 0.2081 REMARK 3 S31: 0.2509 S32: -0.1515 S33: -0.0334 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN B AND RESID 77:162 REMARK 3 ORIGIN FOR THE GROUP (A): -16.3325 11.2367 30.8838 REMARK 3 T TENSOR REMARK 3 T11: 0.3928 T22: 0.5365 REMARK 3 T33: 0.5639 T12: 0.0450 REMARK 3 T13: 0.0008 T23: -0.1006 REMARK 3 L TENSOR REMARK 3 L11: 2.9078 L22: 3.2601 REMARK 3 L33: 3.5065 L12: -1.4373 REMARK 3 L13: 0.5348 L23: 0.7070 REMARK 3 S TENSOR REMARK 3 S11: 0.2518 S12: 0.5395 S13: -0.2935 REMARK 3 S21: -0.3460 S22: -0.2626 S23: 0.2850 REMARK 3 S31: 0.0916 S32: -0.1173 S33: 0.0638 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN B AND RESID 1:76 REMARK 3 ORIGIN FOR THE GROUP (A): 3.9532 7.8365 38.0575 REMARK 3 T TENSOR REMARK 3 T11: 0.4297 T22: 0.4850 REMARK 3 T33: 0.3288 T12: 0.0591 REMARK 3 T13: 0.0320 T23: 0.0143 REMARK 3 L TENSOR REMARK 3 L11: 3.8960 L22: 3.5891 REMARK 3 L33: 2.9550 L12: 0.5724 REMARK 3 L13: 0.5455 L23: 0.9793 REMARK 3 S TENSOR REMARK 3 S11: 0.1037 S12: -0.6185 S13: 0.0405 REMARK 3 S21: 0.1192 S22: -0.1073 S23: 0.2620 REMARK 3 S31: -0.0761 S32: 0.0990 S33: 0.0556 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN B AND RESID 163:388 REMARK 3 ORIGIN FOR THE GROUP (A): 32.5308 10.2760 19.8653 REMARK 3 T TENSOR REMARK 3 T11: 0.2977 T22: 0.2102 REMARK 3 T33: 0.2377 T12: -0.0720 REMARK 3 T13: -0.0223 T23: 0.0276 REMARK 3 L TENSOR REMARK 3 L11: 2.9902 L22: 2.2381 REMARK 3 L33: 2.8262 L12: 0.0306 REMARK 3 L13: -0.3439 L23: 0.5051 REMARK 3 S TENSOR REMARK 3 S11: -0.0180 S12: -0.0512 S13: 0.2580 REMARK 3 S21: -0.1026 S22: -0.0218 S23: -0.1855 REMARK 3 S31: -0.5487 S32: 0.3819 S33: 0.0170 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN C REMARK 3 ORIGIN FOR THE GROUP (A): -3.8566 -9.8409 33.4761 REMARK 3 T TENSOR REMARK 3 T11: 1.3167 T22: 0.8890 REMARK 3 T33: 1.3669 T12: -0.0200 REMARK 3 T13: -0.1689 T23: -0.0464 REMARK 3 L TENSOR REMARK 3 L11: 2.7760 L22: 3.0825 REMARK 3 L33: 1.3485 L12: -1.4371 REMARK 3 L13: 0.2147 L23: 0.3175 REMARK 3 S TENSOR REMARK 3 S11: 0.5531 S12: 0.1850 S13: -1.3617 REMARK 3 S21: 0.2154 S22: -0.3370 S23: 0.4309 REMARK 3 S31: 0.7285 S32: 0.2314 S33: -0.2354 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): 26.2395 25.5874 -5.4205 REMARK 3 T TENSOR REMARK 3 T11: 0.8939 T22: 1.2246 REMARK 3 T33: 1.0815 T12: -0.0675 REMARK 3 T13: 0.0698 T23: 0.0959 REMARK 3 L TENSOR REMARK 3 L11: 1.8741 L22: 0.8158 REMARK 3 L33: 1.7800 L12: -0.6418 REMARK 3 L13: 1.7077 L23: -0.2213 REMARK 3 S TENSOR REMARK 3 S11: -0.5503 S12: -0.2369 S13: -0.1289 REMARK 3 S21: 0.1704 S22: 0.1067 S23: -0.4992 REMARK 3 S31: -0.2192 S32: 0.4304 S33: 0.3460 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 3 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: ((CHAIN A AND (RESID 4:10 OR RESID 24:45 REMARK 3 OR RESID 46:62 OR RESID 63:75 ) AND (NAME REMARK 3 CA OR NAME N OR NAME C OR NAME O )) OR REMARK 3 (CHAIN A AND (RESID 4 OR RESID 6:10 OR REMARK 3 RESID 24:25 OR RESID 27:28 OR RESID 31:40 REMARK 3 OR RESID 44:52 OR RESID 54:62 OR RESID 63: REMARK 3 67 OR RESID 70 OR RESID 72:74 ) AND NOT REMARK 3 (NAME CA OR NAME N OR NAME C OR NAME O))) REMARK 3 SELECTION : ((CHAIN B AND (RESID 4:10 OR RESID 24:45 REMARK 3 OR RESID 46:62 OR RESID 63:75 ) AND (NAME REMARK 3 CA OR NAME N OR NAME C OR NAME O )) OR REMARK 3 (CHAIN B AND (RESID 4 OR RESID 6:10 OR REMARK 3 RESID 24:25 OR RESID 27:28 OR RESID 31:40 REMARK 3 OR RESID 44:52 OR RESID 54:62 OR RESID 63: REMARK 3 67 OR RESID 70 OR RESID 72:74 ) AND NOT REMARK 3 (NAME CA OR NAME N OR NAME C OR NAME O))) REMARK 3 ATOM PAIRS NUMBER : 438 REMARK 3 RMSD : 0.323 REMARK 3 NCS GROUP : 2 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: ((CHAIN A AND (RESID 76:109 OR RESID 114: REMARK 3 137 OR RESID 138:159 ) AND (NAME CA OR REMARK 3 NAME N OR NAME C OR NAME O) ) OR (SEGID A REMARK 3 AND (RESID 76:81 OR RESID 83:84 OR RESID REMARK 3 86:91 OR RESID 93:96 OR RESID 98:100 OR REMARK 3 RESID 103:109 OR RESID 114 OR RESID 116: REMARK 3 118 OR RESID 121:130 OR RESID 132:133 OR REMARK 3 RESID 135:140 OR RESID 143:157 OR RESID REMARK 3 159) AND NOT (NAME CA OR NAME N OR NAME C REMARK 3 OR NAME O) ) ) REMARK 3 SELECTION : ((CHAIN B AND (RESID 76:109 OR RESID 114: REMARK 3 137 OR RESID 138:159 ) AND (NAME CA OR REMARK 3 NAME N OR NAME C OR NAME O) ) OR (SEGID B REMARK 3 AND (RESID 76:81 OR RESID 83:84 OR RESID REMARK 3 86:91 OR RESID 93:96 OR RESID 98:100 OR REMARK 3 RESID 103:109 OR RESID 114 OR RESID 116: REMARK 3 118 OR RESID 121:130 OR RESID 132:133 OR REMARK 3 RESID 135:140 OR RESID 143:157 OR RESID REMARK 3 159) AND NOT (NAME CA OR NAME N OR NAME C REMARK 3 OR NAME O) ) ) REMARK 3 ATOM PAIRS NUMBER : 580 REMARK 3 RMSD : 0.354 REMARK 3 NCS GROUP : 3 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: ((CHAIN A AND (RESID 167:181 OR RESID REMARK 3 182:209 OR RESID 216:246 OR RESID 247:323 REMARK 3 OR RESID 324:336 OR RESID 351:356 OR REMARK 3 RESID 357:367 OR RESID 371:387) AND (NAME REMARK 3 CA OR NAME N OR NAME C OR NAME O)) OR REMARK 3 (SEGID A AND (RESID 167:181 OR RESID 182: REMARK 3 209 OR RESID 216:244 OR RESID 246:256 OR REMARK 3 RESID 258:319 OR RESID 321:324 OR RESID REMARK 3 326:332 OR RESID 351:354 OR RESID 356:361 REMARK 3 OR RESID 363:367 OR RESID 371:376 OR REMARK 3 RESID 378:382 OR RESID 384:387 ) AND NOT REMARK 3 (NAME CA OR NAME N OR NAME C OR NAME O)) ) REMARK 3 SELECTION : ((CHAIN B AND (RESID 167:181 OR RESID REMARK 3 182:209 OR RESID 216:246 OR RESID 247:323 REMARK 3 OR RESID 324:336 OR RESID 351:356 OR REMARK 3 RESID 357:367 OR RESID 371:387) AND (NAME REMARK 3 CA OR NAME N OR NAME C OR NAME O)) OR REMARK 3 (SEGID B AND (RESID 167:181 OR RESID 182: REMARK 3 209 OR RESID 216:244 OR RESID 246:256 OR REMARK 3 RESID 258:319 OR RESID 321:324 OR RESID REMARK 3 326:332 OR RESID 351:354 OR RESID 356:361 REMARK 3 OR RESID 363:367 OR RESID 371:376 OR REMARK 3 RESID 378:382 OR RESID 384:387 ) AND NOT REMARK 3 (NAME CA OR NAME N OR NAME C OR NAME O)) ) REMARK 3 ATOM PAIRS NUMBER : 1484 REMARK 3 RMSD : 0.316 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4KR6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000079691. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-06 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 : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.008500 REMARK 200 MONOCHROMATOR : GRAPHITE, REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30547 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.4200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.62600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.060 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: 2C5S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 MICRO-LITER OF THII-RNA COMPLEX REMARK 280 SOLUTION AT 10 MG/ML IN A BUFFER CONSISTING OF 150 MM AMMONIUM REMARK 280 SULFATE, 20MM TRIS/HCL PH 7.5 WAS MIXED WITH 3 MICRO-LITER OF REMARK 280 FRESHLY PREPARED RESERVOIR SOLUTION (2.0 M SODIUM FORMATE, 100 REMARK 280 MM SODIUM CITRATE, 2 MMDTT), VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 292K, PH 4.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 50.32600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.65650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.16250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.65650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 50.32600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.16250 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: TETRAMERIC 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O TYR A 166 O HOH A 506 2.02 REMARK 500 O ILE A 32 OG1 THR A 36 2.06 REMARK 500 O ASP B 256 OG SER B 259 2.09 REMARK 500 O PRO A 170 OG1 THR A 173 2.09 REMARK 500 O ASP A 256 OG SER A 259 2.13 REMARK 500 O GLU A 377 OG SER A 381 2.14 REMARK 500 OG SER B 77 OE1 GLU B 82 2.14 REMARK 500 O ILE A 64 O HOH A 506 2.16 REMARK 500 O VAL B 83 OG SER B 87 2.17 REMARK 500 OG SER B 208 OE1 GLN B 247 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 G D 1 P G D 1 OP3 -0.131 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 16 -11.23 72.85 REMARK 500 ASN A 54 18.44 57.24 REMARK 500 GLU A 113 49.08 -92.51 REMARK 500 ASP A 342 -156.56 -123.59 REMARK 500 CYS A 344 -17.46 71.85 REMARK 500 VAL A 345 22.42 41.28 REMARK 500 LYS B 19 34.10 -86.62 REMARK 500 ASP B 79 108.04 -59.91 REMARK 500 LYS B 112 -115.44 63.37 REMARK 500 GLU B 113 86.24 -68.81 REMARK 500 ASP B 161 178.00 56.36 REMARK 500 SER B 305 -7.46 -59.12 REMARK 500 PRO B 339 64.82 -12.14 REMARK 500 CYS B 344 87.89 -163.24 REMARK 500 LYS B 350 -8.66 63.11 REMARK 500 ASN B 351 65.51 -162.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG B 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4KR7 RELATED DB: PDB REMARK 900 RELATED ID: 4KR9 RELATED DB: PDB DBREF 4KR6 A 1 388 UNP Q9X220 THII_THEMA 1 388 DBREF 4KR6 B 1 388 UNP Q9X220 THII_THEMA 1 388 DBREF 4KR6 C 1 39 PDB 4KR6 4KR6 1 39 DBREF 4KR6 D 1 39 PDB 4KR6 4KR6 1 39 SEQADV 4KR6 GLU A 2 UNP Q9X220 LYS 2 ENGINEERED MUTATION SEQADV 4KR6 GLU B 2 UNP Q9X220 LYS 2 ENGINEERED MUTATION SEQRES 1 A 388 MET GLU GLU LEU ARG VAL TYR ILE VAL ARG TYR SER GLU SEQRES 2 A 388 ILE GLY LEU LYS GLY LYS ASN ARG LYS ASP PHE GLU GLU SEQRES 3 A 388 ALA LEU ARG ARG ASN ILE GLU ARG VAL THR GLY MET LYS SEQRES 4 A 388 VAL LYS ARG GLN TRP GLY ARG PHE LEU ILE PRO ILE ASP SEQRES 5 A 388 GLU ASN VAL THR LEU ASP ASP LYS LEU LYS LYS ILE PHE SEQRES 6 A 388 GLY ILE GLN ASN PHE SER LYS GLY PHE LEU VAL SER HIS SEQRES 7 A 388 ASP PHE GLU GLU VAL LYS LYS TYR SER LEU ILE ALA VAL SEQRES 8 A 388 LYS GLU LYS LEU GLU LYS GLY ASN TYR ARG THR PHE LYS SEQRES 9 A 388 VAL GLN ALA LYS LYS ALA TYR LYS GLU TYR LYS LYS GLY SEQRES 10 A 388 VAL TYR GLU ILE ASN SER GLU LEU GLY ALA LEU ILE LEU SEQRES 11 A 388 LYS ASN PHE LYS GLU LEU SER VAL ASP VAL ARG ASN PRO SEQRES 12 A 388 ASP PHE VAL LEU GLY VAL GLU VAL ARG PRO GLU GLY VAL SEQRES 13 A 388 LEU ILE PHE THR ASP ARG VAL GLU CYS TYR GLY GLY LEU SEQRES 14 A 388 PRO VAL GLY THR GLY GLY LYS ALA VAL LEU LEU LEU SER SEQRES 15 A 388 GLY GLY ILE ASP SER PRO VAL ALA GLY TRP TYR ALA LEU SEQRES 16 A 388 LYS ARG GLY VAL LEU ILE GLU SER VAL THR PHE VAL SER SEQRES 17 A 388 PRO PRO PHE THR SER GLU GLY ALA VAL GLU LYS VAL ARG SEQRES 18 A 388 ASP ILE LEU ARG VAL LEU ARG GLU PHE SER GLY GLY HIS SEQRES 19 A 388 PRO LEU ARG LEU HIS ILE VAL ASN LEU THR LYS LEU GLN SEQRES 20 A 388 LEU GLU VAL LYS LYS ARG VAL PRO ASP LYS TYR SER LEU SEQRES 21 A 388 ILE MET TYR ARG ARG SER MET PHE ARG ILE ALA GLU LYS SEQRES 22 A 388 ILE ALA GLU GLU THR GLY ALA VAL ALA PHE TYR THR GLY SEQRES 23 A 388 GLU ASN ILE GLY GLN VAL ALA SER GLN THR LEU GLU ASN SEQRES 24 A 388 LEU TRP SER ILE GLU SER VAL THR THR ARG PRO VAL ILE SEQRES 25 A 388 ARG PRO LEU SER GLY PHE ASP LYS THR GLU ILE VAL GLU SEQRES 26 A 388 LYS ALA LYS GLU ILE GLY THR TYR GLU ILE SER ILE LYS SEQRES 27 A 388 PRO TYR GLN ASP SER CYS VAL PHE PHE ALA PRO LYS ASN SEQRES 28 A 388 PRO ALA THR ARG SER HIS PRO SER ILE LEU GLU LYS LEU SEQRES 29 A 388 GLU GLN GLN VAL PRO ASP LEU PRO VAL LEU GLU GLU GLU SEQRES 30 A 388 ALA PHE THR SER ARG LYS VAL GLU VAL ILE GLU SEQRES 1 B 388 MET GLU GLU LEU ARG VAL TYR ILE VAL ARG TYR SER GLU SEQRES 2 B 388 ILE GLY LEU LYS GLY LYS ASN ARG LYS ASP PHE GLU GLU SEQRES 3 B 388 ALA LEU ARG ARG ASN ILE GLU ARG VAL THR GLY MET LYS SEQRES 4 B 388 VAL LYS ARG GLN TRP GLY ARG PHE LEU ILE PRO ILE ASP SEQRES 5 B 388 GLU ASN VAL THR LEU ASP ASP LYS LEU LYS LYS ILE PHE SEQRES 6 B 388 GLY ILE GLN ASN PHE SER LYS GLY PHE LEU VAL SER HIS SEQRES 7 B 388 ASP PHE GLU GLU VAL LYS LYS TYR SER LEU ILE ALA VAL SEQRES 8 B 388 LYS GLU LYS LEU GLU LYS GLY ASN TYR ARG THR PHE LYS SEQRES 9 B 388 VAL GLN ALA LYS LYS ALA TYR LYS GLU TYR LYS LYS GLY SEQRES 10 B 388 VAL TYR GLU ILE ASN SER GLU LEU GLY ALA LEU ILE LEU SEQRES 11 B 388 LYS ASN PHE LYS GLU LEU SER VAL ASP VAL ARG ASN PRO SEQRES 12 B 388 ASP PHE VAL LEU GLY VAL GLU VAL ARG PRO GLU GLY VAL SEQRES 13 B 388 LEU ILE PHE THR ASP ARG VAL GLU CYS TYR GLY GLY LEU SEQRES 14 B 388 PRO VAL GLY THR GLY GLY LYS ALA VAL LEU LEU LEU SER SEQRES 15 B 388 GLY GLY ILE ASP SER PRO VAL ALA GLY TRP TYR ALA LEU SEQRES 16 B 388 LYS ARG GLY VAL LEU ILE GLU SER VAL THR PHE VAL SER SEQRES 17 B 388 PRO PRO PHE THR SER GLU GLY ALA VAL GLU LYS VAL ARG SEQRES 18 B 388 ASP ILE LEU ARG VAL LEU ARG GLU PHE SER GLY GLY HIS SEQRES 19 B 388 PRO LEU ARG LEU HIS ILE VAL ASN LEU THR LYS LEU GLN SEQRES 20 B 388 LEU GLU VAL LYS LYS ARG VAL PRO ASP LYS TYR SER LEU SEQRES 21 B 388 ILE MET TYR ARG ARG SER MET PHE ARG ILE ALA GLU LYS SEQRES 22 B 388 ILE ALA GLU GLU THR GLY ALA VAL ALA PHE TYR THR GLY SEQRES 23 B 388 GLU ASN ILE GLY GLN VAL ALA SER GLN THR LEU GLU ASN SEQRES 24 B 388 LEU TRP SER ILE GLU SER VAL THR THR ARG PRO VAL ILE SEQRES 25 B 388 ARG PRO LEU SER GLY PHE ASP LYS THR GLU ILE VAL GLU SEQRES 26 B 388 LYS ALA LYS GLU ILE GLY THR TYR GLU ILE SER ILE LYS SEQRES 27 B 388 PRO TYR GLN ASP SER CYS VAL PHE PHE ALA PRO LYS ASN SEQRES 28 B 388 PRO ALA THR ARG SER HIS PRO SER ILE LEU GLU LYS LEU SEQRES 29 B 388 GLU GLN GLN VAL PRO ASP LEU PRO VAL LEU GLU GLU GLU SEQRES 30 B 388 ALA PHE THR SER ARG LYS VAL GLU VAL ILE GLU SEQRES 1 C 39 G C C C G G A U A G U G U SEQRES 2 C 39 C C U U G G G A A A C C A SEQRES 3 C 39 A G U C C G G G C A C C A SEQRES 1 D 39 G C C C G G A U A G U G U SEQRES 2 D 39 C C U U G G G A A A C C A SEQRES 3 D 39 A G U C C G G G C A C C A HET HG A 401 1 HET HG A 402 1 HET HG A 403 1 HET HG B 401 1 HETNAM HG MERCURY (II) ION FORMUL 5 HG 4(HG 2+) FORMUL 9 HOH *75(H2 O) HELIX 1 1 TYR A 11 GLY A 15 5 5 HELIX 2 2 ASN A 20 GLY A 37 1 18 HELIX 3 3 LEU A 57 LYS A 62 1 6 HELIX 4 4 ASP A 79 GLU A 96 1 18 HELIX 5 5 GLY A 117 PHE A 133 1 17 HELIX 6 6 ILE A 185 ARG A 197 1 13 HELIX 7 7 GLY A 215 ARG A 228 1 14 HELIX 8 8 GLU A 229 SER A 231 5 3 HELIX 9 9 LEU A 243 VAL A 254 1 12 HELIX 10 10 PRO A 255 LYS A 257 5 3 HELIX 11 11 TYR A 258 GLY A 279 1 22 HELIX 12 12 VAL A 292 GLN A 295 5 4 HELIX 13 13 THR A 296 SER A 305 1 10 HELIX 14 14 ASP A 319 ILE A 330 1 12 HELIX 15 15 HIS A 357 GLU A 365 1 9 HELIX 16 16 GLN A 366 VAL A 368 5 3 HELIX 17 17 ASP A 370 SER A 381 1 12 HELIX 18 18 ASP B 23 GLY B 37 1 15 HELIX 19 19 LEU B 57 LYS B 62 1 6 HELIX 20 20 ASP B 79 GLU B 96 1 18 HELIX 21 21 GLY B 117 PHE B 133 1 17 HELIX 22 22 ILE B 185 ARG B 197 1 13 HELIX 23 23 GLY B 215 ARG B 228 1 14 HELIX 24 24 GLU B 229 SER B 231 5 3 HELIX 25 25 LEU B 243 VAL B 254 1 12 HELIX 26 26 PRO B 255 GLY B 279 1 25 HELIX 27 27 VAL B 292 GLN B 295 5 4 HELIX 28 28 THR B 296 SER B 305 1 10 HELIX 29 29 ASP B 319 GLY B 331 1 13 HELIX 30 30 ILE B 337 GLN B 341 5 5 HELIX 31 31 HIS B 357 GLU B 365 1 9 HELIX 32 32 GLN B 366 VAL B 368 5 3 HELIX 33 33 ASP B 370 SER B 381 1 12 SHEET 1 A 8 LYS A 41 GLN A 43 0 SHEET 2 A 8 ARG A 46 PRO A 50 -1 O ARG A 46 N GLN A 43 SHEET 3 A 8 LEU A 4 ARG A 10 -1 N VAL A 9 O PHE A 47 SHEET 4 A 8 ASN A 69 VAL A 76 -1 O ASN A 69 N ARG A 10 SHEET 5 A 8 GLY A 155 ARG A 162 -1 O ILE A 158 N PHE A 74 SHEET 6 A 8 PHE A 145 ARG A 152 -1 N GLU A 150 O LEU A 157 SHEET 7 A 8 THR A 102 LYS A 109 1 N LYS A 104 O LEU A 147 SHEET 8 A 8 SER A 137 VAL A 138 1 O SER A 137 N PHE A 103 SHEET 1 B 6 VAL A 311 ILE A 312 0 SHEET 2 B 6 PHE A 283 TYR A 284 1 N PHE A 283 O ILE A 312 SHEET 3 B 6 LYS A 176 LEU A 180 1 N LEU A 180 O TYR A 284 SHEET 4 B 6 LEU A 200 VAL A 207 1 O GLU A 202 N ALA A 177 SHEET 5 B 6 LEU A 236 ASN A 242 1 O ARG A 237 N SER A 203 SHEET 6 B 6 LYS A 383 ILE A 387 -1 O LYS A 383 N ILE A 240 SHEET 1 C 8 LYS B 41 GLN B 43 0 SHEET 2 C 8 ARG B 46 PRO B 50 -1 O LEU B 48 N LYS B 41 SHEET 3 C 8 LEU B 4 ARG B 10 -1 N VAL B 9 O PHE B 47 SHEET 4 C 8 ASN B 69 VAL B 76 -1 O SER B 71 N ILE B 8 SHEET 5 C 8 GLY B 155 THR B 160 -1 O ILE B 158 N PHE B 74 SHEET 6 C 8 PHE B 145 ARG B 152 -1 N GLU B 150 O LEU B 157 SHEET 7 C 8 THR B 102 LYS B 109 1 N LYS B 108 O VAL B 149 SHEET 8 C 8 SER B 137 VAL B 138 1 O SER B 137 N PHE B 103 SHEET 1 D 5 LYS B 41 GLN B 43 0 SHEET 2 D 5 ARG B 46 PRO B 50 -1 O LEU B 48 N LYS B 41 SHEET 3 D 5 LEU B 4 ARG B 10 -1 N VAL B 9 O PHE B 47 SHEET 4 D 5 ASN B 69 VAL B 76 -1 O SER B 71 N ILE B 8 SHEET 5 D 5 VAL B 163 GLU B 164 -1 O VAL B 163 N PHE B 70 SHEET 1 E 6 VAL B 311 ILE B 312 0 SHEET 2 E 6 ALA B 282 TYR B 284 1 N PHE B 283 O ILE B 312 SHEET 3 E 6 LYS B 176 LEU B 180 1 N VAL B 178 O ALA B 282 SHEET 4 E 6 LEU B 200 VAL B 207 1 O VAL B 204 N LEU B 179 SHEET 5 E 6 LEU B 236 ASN B 242 1 O HIS B 239 N SER B 203 SHEET 6 E 6 LYS B 383 ILE B 387 -1 O LYS B 383 N ILE B 240 LINK SG CYS B 344 HG HG B 401 1555 1555 2.39 CISPEP 1 PRO A 209 PRO A 210 0 6.16 CISPEP 2 LYS A 338 PRO A 339 0 -17.74 CISPEP 3 PRO B 209 PRO B 210 0 5.49 SITE 1 AC1 2 TYR A 166 GLU A 329 SITE 1 AC2 3 CYS A 344 ILE B 89 LYS B 92 SITE 1 AC3 1 CYS B 344 CRYST1 100.652 110.325 119.313 90.00 90.00 90.00 P 21 21 21 8 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 0.009935 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009064 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008381 0.00000 MTRIX1 1 0.441970 -0.804303 0.397190 5.71677 1 MTRIX2 1 -0.807845 -0.549359 -0.213519 21.39550 1 MTRIX3 1 0.389934 -0.226499 -0.892552 22.48940 1 MTRIX1 2 0.499903 -0.797086 0.338749 8.28537 1 MTRIX2 2 -0.804237 -0.572374 -0.159973 19.50290 1 MTRIX3 2 0.321403 -0.192464 -0.927177 22.90450 1 MTRIX1 3 0.567138 -0.741477 0.358561 4.09714 1 MTRIX2 3 -0.744880 -0.647521 -0.160842 19.67030 1 MTRIX3 3 0.351436 -0.175866 -0.919545 23.62330 1