HEADER TRANSFERASE/RNA 02-JUL-15 5CCX TITLE STRUCTURE OF THE PRODUCT COMPLEX OF TRNA M1A58 METHYLTRANSFERASE WITH TITLE 2 TRNA3LYS AS SUBSTRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA (ADENINE(58)-N(1))-METHYLTRANSFERASE CATALYTIC SUBUNIT COMPND 3 TRMT61A; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: TRNA(M1A58)-METHYLTRANSFERASE SUBUNIT TRMT61A,TRNA(M1A58) COMPND 6 MTASE SUBUNIT TRMT61A; COMPND 7 EC: 2.1.1.220; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: TRNA (ADENINE(58)-N(1))-METHYLTRANSFERASE NON-CATALYTIC COMPND 11 SUBUNIT TRM6; COMPND 12 CHAIN: B; COMPND 13 SYNONYM: TRNA(M1A58)-METHYLTRANSFERASE SUBUNIT TRM6,TRNA(M1A58)MTASE COMPND 14 SUBUNIT TRM6; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 3; COMPND 17 MOLECULE: TRNA3LYS; COMPND 18 CHAIN: N; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TRMT61A, C14ORF172, TRM61; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET17B-6HISTRM6-TRM61; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: TRMT6, KIAA1153, TRM6, CGI-09; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 17 EXPRESSION_SYSTEM_CELL_LINE: BL21(DE3); SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET17B-6HISTRM6-TRM61; SOURCE 19 MOL_ID: 3; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 22 ORGANISM_COMMON: HUMAN; SOURCE 23 ORGANISM_TAXID: 9606 KEYWDS TRNA MODIFICATION, SAM-DEPENDENT METHYLTRANSFERASE CLASS I, KEYWDS 2 METHYLTRANSFERASE FOLD, HIV-1 PRIMER, TRANSFERASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.FINER-MOORE,N.CZUDNOCHOWSKI,J.D.O'CONNELL III,A.L.WANG,R.M.STROUD REVDAT 5 27-SEP-23 5CCX 1 LINK REVDAT 4 25-DEC-19 5CCX 1 REMARK REVDAT 3 27-SEP-17 5CCX 1 JRNL REMARK REVDAT 2 16-DEC-15 5CCX 1 JRNL REVDAT 1 04-NOV-15 5CCX 0 JRNL AUTH J.FINER-MOORE,N.CZUDNOCHOWSKI,J.D.O'CONNELL,A.L.WANG, JRNL AUTH 2 R.M.STROUD JRNL TITL CRYSTAL STRUCTURE OF THE HUMAN TRNA M(1)A58 JRNL TITL 2 METHYLTRANSFERASE-TRNA3(LYS) COMPLEX: REFOLDING OF SUBSTRATE JRNL TITL 3 TRNA ALLOWS ACCESS TO THE METHYLATION TARGET. JRNL REF J.MOL.BIOL. V. 427 3862 2015 JRNL REFN ESSN 1089-8638 JRNL PMID 26470919 JRNL DOI 10.1016/J.JMB.2015.10.005 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 98079 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 4963 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 54.1487 - 6.5215 0.99 3360 177 0.1870 0.1725 REMARK 3 2 6.5215 - 5.1776 1.00 3221 184 0.1930 0.2099 REMARK 3 3 5.1776 - 4.5235 1.00 3180 163 0.1603 0.2083 REMARK 3 4 4.5235 - 4.1101 1.00 3139 178 0.1570 0.1942 REMARK 3 5 4.1101 - 3.8156 1.00 3152 160 0.1679 0.1957 REMARK 3 6 3.8156 - 3.5907 1.00 3125 163 0.1828 0.2165 REMARK 3 7 3.5907 - 3.4109 1.00 3123 169 0.1968 0.2280 REMARK 3 8 3.4109 - 3.2624 1.00 3117 172 0.2061 0.2417 REMARK 3 9 3.2624 - 3.1368 1.00 3118 154 0.2091 0.2159 REMARK 3 10 3.1368 - 3.0286 1.00 3078 183 0.2047 0.2653 REMARK 3 11 3.0286 - 2.9339 1.00 3095 151 0.2309 0.2832 REMARK 3 12 2.9339 - 2.8501 1.00 3078 175 0.2223 0.3032 REMARK 3 13 2.8501 - 2.7750 1.00 3110 167 0.2325 0.2864 REMARK 3 14 2.7750 - 2.7073 1.00 3097 162 0.2405 0.2858 REMARK 3 15 2.7073 - 2.6458 1.00 3082 161 0.2429 0.2834 REMARK 3 16 2.6458 - 2.5895 1.00 3057 184 0.2334 0.2387 REMARK 3 17 2.5895 - 2.5377 1.00 3084 165 0.2484 0.2665 REMARK 3 18 2.5377 - 2.4898 1.00 3061 163 0.2505 0.3172 REMARK 3 19 2.4898 - 2.4453 1.00 3099 156 0.2570 0.2810 REMARK 3 20 2.4453 - 2.4039 1.00 3049 158 0.2572 0.3035 REMARK 3 21 2.4039 - 2.3651 1.00 3103 165 0.2715 0.3230 REMARK 3 22 2.3651 - 2.3287 1.00 3057 149 0.2784 0.2789 REMARK 3 23 2.3287 - 2.2945 1.00 3095 173 0.2870 0.3549 REMARK 3 24 2.2945 - 2.2621 1.00 3056 162 0.2897 0.3192 REMARK 3 25 2.2621 - 2.2316 1.00 3058 183 0.2953 0.3390 REMARK 3 26 2.2316 - 2.2026 1.00 3041 163 0.3013 0.3025 REMARK 3 27 2.2026 - 2.1751 1.00 3070 153 0.3091 0.3444 REMARK 3 28 2.1751 - 2.1489 1.00 3068 162 0.3263 0.3880 REMARK 3 29 2.1489 - 2.1239 1.00 3079 175 0.3258 0.3463 REMARK 3 30 2.1239 - 2.1000 1.00 3064 133 0.3321 0.3582 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.250 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 : 0.004 7172 REMARK 3 ANGLE : 0.699 10099 REMARK 3 CHIRALITY : 0.039 1189 REMARK 3 PLANARITY : 0.003 995 REMARK 3 DIHEDRAL : 14.173 2899 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5CCX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211382. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-SEP-14 REMARK 200 TEMPERATURE (KELVIN) : 103 REMARK 200 PH : 4.8-5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.11587 REMARK 200 MONOCHROMATOR : DOUBLE FLAT CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 98180 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 108.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : 0.10300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : 2.59000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 5CCB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 MICROLITER PROTEIN SOLUTION (4.8 REMARK 280 MG/ML PROTEIN, 66.4 MICROMOLAR TRNA3LYS, 2MM SAM, 1MM MGCL2 AND REMARK 280 50MM HEPES PH 7.5) PLUS 1 MICROLITER RESERVOIR SOLUTION (0.1 M REMARK 280 NAACETATE, PH 4.8-5.0, 2% W/V PEG 4000 AND 15% V/V MPD) OVER REMARK 280 1000 MICROLITERS RESERVOIR SOLUTION, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 -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 88.58000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 68.38500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 68.38500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 132.87000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 68.38500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 68.38500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 44.29000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 68.38500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 68.38500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 132.87000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 68.38500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 68.38500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 44.29000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 88.58000 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 31380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 68740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -195.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, N 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 THR A 254 REMARK 465 ASP A 255 REMARK 465 GLY A 256 REMARK 465 PRO A 257 REMARK 465 ALA A 258 REMARK 465 GLY A 259 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 GLY B 3 REMARK 465 SER B 4 REMARK 465 GLY B 5 REMARK 465 GLU B 6 REMARK 465 GLN B 7 REMARK 465 PRO B 8 REMARK 465 GLY B 9 REMARK 465 PRO B 10 REMARK 465 GLN B 11 REMARK 465 PRO B 12 REMARK 465 GLN B 13 REMARK 465 HIS B 14 REMARK 465 PRO B 15 REMARK 465 GLY B 16 REMARK 465 ASP B 17 REMARK 465 GLU B 81 REMARK 465 GLU B 82 REMARK 465 PRO B 83 REMARK 465 THR B 84 REMARK 465 ALA B 85 REMARK 465 GLU B 86 REMARK 465 THR B 87 REMARK 465 ALA B 272 REMARK 465 LYS B 273 REMARK 465 MET B 274 REMARK 465 LEU B 275 REMARK 465 SER B 276 REMARK 465 SER B 277 REMARK 465 GLU B 278 REMARK 465 PRO B 279 REMARK 465 LYS B 280 REMARK 465 ASP B 281 REMARK 465 SER B 282 REMARK 465 ALA B 283 REMARK 465 LEU B 284 REMARK 465 VAL B 285 REMARK 465 GLU B 286 REMARK 465 GLU B 287 REMARK 465 SER B 288 REMARK 465 ASN B 289 REMARK 465 GLY B 290 REMARK 465 THR B 291 REMARK 465 LEU B 292 REMARK 465 GLU B 293 REMARK 465 GLU B 294 REMARK 465 LYS B 295 REMARK 465 GLN B 296 REMARK 465 ALA B 297 REMARK 465 SER B 298 REMARK 465 GLU B 299 REMARK 465 GLN B 300 REMARK 465 GLU B 301 REMARK 465 ASN B 302 REMARK 465 GLU B 303 REMARK 465 ASP B 304 REMARK 465 SER B 305 REMARK 465 MET B 306 REMARK 465 ALA B 307 REMARK 465 GLU B 308 REMARK 465 ALA B 309 REMARK 465 PRO B 310 REMARK 465 GLU B 311 REMARK 465 SER B 312 REMARK 465 ASN B 313 REMARK 465 HIS B 314 REMARK 465 PRO B 315 REMARK 465 GLU B 316 REMARK 465 ASP B 317 REMARK 465 GLN B 318 REMARK 465 GLU B 319 REMARK 465 THR B 320 REMARK 465 MET B 321 REMARK 465 GLU B 322 REMARK 465 THR B 323 REMARK 465 ILE B 324 REMARK 465 SER B 325 REMARK 465 GLN B 326 REMARK 465 ASP B 327 REMARK 465 PRO B 328 REMARK 465 GLU B 329 REMARK 465 HIS B 330 REMARK 465 LYS B 331 REMARK 465 GLY B 332 REMARK 465 PRO B 333 REMARK 465 LYS B 334 REMARK 465 GLU B 335 REMARK 465 ARG B 336 REMARK 465 GLY B 337 REMARK 465 SER B 338 REMARK 465 LYS B 339 REMARK 465 LEU B 464 REMARK 465 LYS B 465 REMARK 465 ALA B 466 REMARK 465 ASP B 467 REMARK 465 THR B 468 REMARK 465 SER B 469 REMARK 465 LEU B 470 REMARK 465 LYS B 471 REMARK 465 SER B 472 REMARK 465 ASN B 473 REMARK 465 ALA B 474 REMARK 465 SER B 475 REMARK 465 THR B 476 REMARK 465 LEU B 477 REMARK 465 GLU B 478 REMARK 465 SER B 479 REMARK 465 HIS B 480 REMARK 465 GLU B 481 REMARK 465 THR B 482 REMARK 465 GLU B 483 REMARK 465 GLU B 484 REMARK 465 PRO B 485 REMARK 465 ALA B 486 REMARK 465 ALA B 487 REMARK 465 LYS B 488 REMARK 465 LYS B 489 REMARK 465 ARG B 490 REMARK 465 LYS B 491 REMARK 465 CYS B 492 REMARK 465 PRO B 493 REMARK 465 GLU B 494 REMARK 465 SER B 495 REMARK 465 ASP B 496 REMARK 465 SER B 497 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 ARG A 62 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 75 CG CD OE1 NE2 REMARK 470 LYS B 77 CG CD CE NZ REMARK 470 LYS B 78 CG CD CE NZ REMARK 470 LYS B 79 CG CD CE NZ REMARK 470 LYS B 120 CG CD CE NZ REMARK 470 LYS B 148 CG CD CE NZ REMARK 470 LYS B 248 CE NZ REMARK 470 LYS B 340 CG CD CE NZ REMARK 470 ASP B 341 CG OD1 OD2 REMARK 470 GLN B 344 CG CD OE1 NE2 REMARK 470 ASN B 463 CG OD1 ND2 REMARK 470 A N 76 C4 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 OP2 C N 17 N2 G N 19 2.01 REMARK 500 OP2 G N 69 O HOH N 201 2.04 REMARK 500 OD1 ASP B 99 O2' G N 53 2.06 REMARK 500 NH2 ARG B 220 O HOH B 501 2.11 REMARK 500 O HOH B 568 O HOH B 593 2.13 REMARK 500 OP2 U N 34 O HOH N 202 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 405 O HOH A 405 7555 2.14 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 HIS A 22 -121.96 62.34 REMARK 500 CYS A 60 -76.68 -101.91 REMARK 500 ARG A 62 41.28 -80.24 REMARK 500 ASP A 261 33.08 -90.89 REMARK 500 THR A 262 26.98 -145.41 REMARK 500 THR A 278 -68.77 -95.04 REMARK 500 GLU B 31 -90.49 -114.92 REMARK 500 LYS B 49 47.77 72.04 REMARK 500 THR B 69 -68.83 -145.87 REMARK 500 LYS B 105 35.45 -92.82 REMARK 500 LYS B 120 -71.21 -43.78 REMARK 500 GLU B 155 69.07 -104.51 REMARK 500 GLU B 176 58.28 -143.26 REMARK 500 ARG B 238 30.69 -140.90 REMARK 500 THR B 269 31.14 -90.86 REMARK 500 LYS B 443 -78.42 -103.79 REMARK 500 REMARK 500 REMARK: NULL 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 NA N 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U N 8 OP1 REMARK 620 2 A N 9 OP2 89.8 REMARK 620 3 HOH N 217 O 86.4 166.4 REMARK 620 4 HOH N 239 O 78.4 83.1 83.4 REMARK 620 5 HOH N 263 O 163.2 92.9 87.0 85.4 REMARK 620 6 HOH N 269 O 94.2 94.9 98.4 172.3 102.1 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 SAH A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA N 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CCB RELATED DB: PDB REMARK 900 RELATED ID: 5CD1 RELATED DB: PDB DBREF 5CCX A 1 289 UNP Q96FX7 TRM61_HUMAN 1 289 DBREF 5CCX B 1 497 UNP Q9UJA5 TRM6_HUMAN 1 497 DBREF 5CCX N 0 73 GB 339572 M17620.1 1340 1267 SEQADV 5CCX C N 74 GB 339572 INSERTION SEQADV 5CCX C N 75 GB 339572 INSERTION SEQADV 5CCX A N 76 GB 339572 INSERTION SEQRES 1 A 289 MET SER PHE VAL ALA TYR GLU GLU LEU ILE LYS GLU GLY SEQRES 2 A 289 ASP THR ALA ILE LEU SER LEU GLY HIS GLY ALA MET VAL SEQRES 3 A 289 ALA VAL ARG VAL GLN ARG GLY ALA GLN THR GLN THR ARG SEQRES 4 A 289 HIS GLY VAL LEU ARG HIS SER VAL ASP LEU ILE GLY ARG SEQRES 5 A 289 PRO PHE GLY SER LYS VAL THR CYS GLY ARG GLY GLY TRP SEQRES 6 A 289 VAL TYR VAL LEU HIS PRO THR PRO GLU LEU TRP THR LEU SEQRES 7 A 289 ASN LEU PRO HIS ARG THR GLN ILE LEU TYR SER THR ASP SEQRES 8 A 289 ILE ALA LEU ILE THR MET MET LEU GLU LEU ARG PRO GLY SEQRES 9 A 289 SER VAL VAL CYS GLU SER GLY THR GLY SER GLY SER VAL SEQRES 10 A 289 SER HIS ALA ILE ILE ARG THR ILE ALA PRO THR GLY HIS SEQRES 11 A 289 LEU HIS THR VAL GLU PHE HIS GLN GLN ARG ALA GLU LYS SEQRES 12 A 289 ALA ARG GLU GLU PHE GLN GLU HIS ARG VAL GLY ARG TRP SEQRES 13 A 289 VAL THR VAL ARG THR GLN ASP VAL CYS ARG SER GLY PHE SEQRES 14 A 289 GLY VAL SER HIS VAL ALA ASP ALA VAL PHE LEU ASP ILE SEQRES 15 A 289 PRO SER PRO TRP GLU ALA VAL GLY HIS ALA TRP ASP ALA SEQRES 16 A 289 LEU LYS VAL GLU GLY GLY ARG PHE CYS SER PHE SER PRO SEQRES 17 A 289 CYS ILE GLU GLN VAL GLN ARG THR CYS GLN ALA LEU ALA SEQRES 18 A 289 ALA ARG GLY PHE SER GLU LEU SER THR LEU GLU VAL LEU SEQRES 19 A 289 PRO GLN VAL TYR ASN VAL ARG THR VAL SER LEU PRO PRO SEQRES 20 A 289 PRO ASP LEU GLY THR GLY THR ASP GLY PRO ALA GLY SER SEQRES 21 A 289 ASP THR SER PRO PHE ARG SER GLY THR PRO MET LYS GLU SEQRES 22 A 289 ALA VAL GLY HIS THR GLY TYR LEU THR PHE ALA THR LYS SEQRES 23 A 289 THR PRO GLY SEQRES 1 B 497 MET GLU GLY SER GLY GLU GLN PRO GLY PRO GLN PRO GLN SEQRES 2 B 497 HIS PRO GLY ASP HIS ARG ILE ARG ASP GLY ASP PHE VAL SEQRES 3 B 497 VAL LEU LYS ARG GLU ASP VAL PHE LYS ALA VAL GLN VAL SEQRES 4 B 497 GLN ARG ARG LYS LYS VAL THR PHE GLU LYS GLN TRP PHE SEQRES 5 B 497 TYR LEU ASP ASN VAL ILE GLY HIS SER TYR GLY THR ALA SEQRES 6 B 497 PHE GLU VAL THR SER GLY GLY SER LEU GLN PRO LYS LYS SEQRES 7 B 497 LYS ARG GLU GLU PRO THR ALA GLU THR LYS GLU ALA GLY SEQRES 8 B 497 THR ASP ASN ARG ASN ILE VAL ASP ASP GLY LYS SER GLN SEQRES 9 B 497 LYS LEU THR GLN ASP ASP ILE LYS ALA LEU LYS ASP LYS SEQRES 10 B 497 GLY ILE LYS GLY GLU GLU ILE VAL GLN GLN LEU ILE GLU SEQRES 11 B 497 ASN SER THR THR PHE ARG ASP LYS THR GLU PHE ALA GLN SEQRES 12 B 497 ASP LYS TYR ILE LYS LYS LYS LYS LYS LYS TYR GLU ALA SEQRES 13 B 497 ILE ILE THR VAL VAL LYS PRO SER THR ARG ILE LEU SER SEQRES 14 B 497 ILE MET TYR TYR ALA ARG GLU PRO GLY LYS ILE ASN HIS SEQRES 15 B 497 MET ARG TYR ASP THR LEU ALA GLN MET LEU THR LEU GLY SEQRES 16 B 497 ASN ILE ARG ALA GLY ASN LYS MET ILE VAL MET GLU THR SEQRES 17 B 497 CYS ALA GLY LEU VAL LEU GLY ALA MET MET GLU ARG MET SEQRES 18 B 497 GLY GLY PHE GLY SER ILE ILE GLN LEU TYR PRO GLY GLY SEQRES 19 B 497 GLY PRO VAL ARG ALA ALA THR ALA CYS PHE GLY PHE PRO SEQRES 20 B 497 LYS SER PHE LEU SER GLY LEU TYR GLU PHE PRO LEU ASN SEQRES 21 B 497 LYS VAL ASP SER LEU LEU HIS GLY THR PHE SER ALA LYS SEQRES 22 B 497 MET LEU SER SER GLU PRO LYS ASP SER ALA LEU VAL GLU SEQRES 23 B 497 GLU SER ASN GLY THR LEU GLU GLU LYS GLN ALA SER GLU SEQRES 24 B 497 GLN GLU ASN GLU ASP SER MET ALA GLU ALA PRO GLU SER SEQRES 25 B 497 ASN HIS PRO GLU ASP GLN GLU THR MET GLU THR ILE SER SEQRES 26 B 497 GLN ASP PRO GLU HIS LYS GLY PRO LYS GLU ARG GLY SER SEQRES 27 B 497 LYS LYS ASP TYR ILE GLN GLU LYS GLN ARG ARG GLN GLU SEQRES 28 B 497 GLU GLN ARG LYS ARG HIS LEU GLU ALA ALA ALA LEU LEU SEQRES 29 B 497 SER GLU ARG ASN ALA ASP GLY LEU ILE VAL ALA SER ARG SEQRES 30 B 497 PHE HIS PRO THR PRO LEU LEU LEU SER LEU LEU ASP PHE SEQRES 31 B 497 VAL ALA PRO SER ARG PRO PHE VAL VAL TYR CYS GLN TYR SEQRES 32 B 497 LYS GLU PRO LEU LEU GLU CYS TYR THR LYS LEU ARG GLU SEQRES 33 B 497 ARG GLY GLY VAL ILE ASN LEU ARG LEU SER GLU THR TRP SEQRES 34 B 497 LEU ARG ASN TYR GLN VAL LEU PRO ASP ARG SER HIS PRO SEQRES 35 B 497 LYS LEU LEU MET SER GLY GLY GLY GLY TYR LEU LEU SER SEQRES 36 B 497 GLY PHE THR VAL ALA MET ASP ASN LEU LYS ALA ASP THR SEQRES 37 B 497 SER LEU LYS SER ASN ALA SER THR LEU GLU SER HIS GLU SEQRES 38 B 497 THR GLU GLU PRO ALA ALA LYS LYS ARG LYS CYS PRO GLU SEQRES 39 B 497 SER ASP SER SEQRES 1 N 77 G G C C C G G A U A G C U SEQRES 2 N 77 C A G U C G G U A G A G C SEQRES 3 N 77 A U C A G A C U U U U A A SEQRES 4 N 77 U C U G A G G G U C C A G SEQRES 5 N 77 G G U U C A 1MA G U C C C U SEQRES 6 N 77 G U U C G G G C G C C A MODRES 5CCX 1MA N 58 A MODIFIED RESIDUE HET 1MA N 58 70 HET SAH A 301 45 HET NA N 101 1 HETNAM 1MA 6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM NA SODIUM ION FORMUL 3 1MA C11 H16 N5 O7 P FORMUL 4 SAH C14 H20 N6 O5 S FORMUL 5 NA NA 1+ FORMUL 6 HOH *309(H2 O) HELIX 1 AA1 HIS A 45 LEU A 49 1 5 HELIX 2 AA2 THR A 72 LEU A 80 1 9 HELIX 3 AA3 TYR A 88 LEU A 99 1 12 HELIX 4 AA4 GLY A 115 ALA A 126 1 12 HELIX 5 AA5 HIS A 137 HIS A 151 1 15 HELIX 6 AA6 VAL A 153 ARG A 155 5 3 HELIX 7 AA7 ASP A 163 GLY A 168 1 6 HELIX 8 AA8 SER A 184 GLU A 187 5 4 HELIX 9 AA9 ALA A 188 LEU A 196 1 9 HELIX 10 AB1 CYS A 209 GLY A 224 1 16 HELIX 11 AB2 ASP B 55 VAL B 57 5 3 HELIX 12 AB3 ASP B 109 LYS B 117 1 9 HELIX 13 AB4 GLY B 121 ASN B 131 1 11 HELIX 14 AB5 THR B 134 LYS B 138 5 5 HELIX 15 AB6 THR B 139 GLU B 155 1 17 HELIX 16 AB7 SER B 164 GLU B 176 1 13 HELIX 17 AB8 PRO B 177 ASN B 181 5 5 HELIX 18 AB9 ARG B 184 GLY B 195 1 12 HELIX 19 AC1 GLY B 211 GLY B 222 1 12 HELIX 20 AC2 ARG B 238 PHE B 244 1 7 HELIX 21 AC3 PRO B 247 LEU B 251 5 5 HELIX 22 AC4 LYS B 261 LEU B 266 1 6 HELIX 23 AC5 ASP B 341 GLU B 366 1 26 HELIX 24 AC6 HIS B 379 LEU B 388 1 10 HELIX 25 AC7 ASP B 389 VAL B 391 5 3 HELIX 26 AC8 LYS B 404 GLY B 418 1 15 SHEET 1 AA1 4 MET A 25 ARG A 29 0 SHEET 2 AA1 4 THR A 15 SER A 19 -1 N LEU A 18 O VAL A 26 SHEET 3 AA1 4 TRP A 65 LEU A 69 -1 O LEU A 69 N ILE A 17 SHEET 4 AA1 4 LYS A 57 THR A 59 -1 N VAL A 58 O VAL A 66 SHEET 1 AA2 2 GLN A 35 THR A 38 0 SHEET 2 AA2 2 GLY A 41 ARG A 44 -1 O GLY A 41 N THR A 38 SHEET 1 AA314 VAL A 157 ARG A 160 0 SHEET 2 AA314 HIS A 130 VAL A 134 1 N LEU A 131 O THR A 158 SHEET 3 AA314 VAL A 106 SER A 110 1 N VAL A 107 O HIS A 132 SHEET 4 AA314 ALA A 177 LEU A 180 1 O PHE A 179 N CYS A 108 SHEET 5 AA314 GLY A 201 SER A 207 1 O PHE A 206 N LEU A 180 SHEET 6 AA314 TYR A 280 LYS A 286 -1 O TYR A 280 N SER A 207 SHEET 7 AA314 SER A 226 VAL A 243 -1 N SER A 229 O PHE A 283 SHEET 8 AA314 VAL B 420 GLN B 434 -1 O TRP B 429 N LEU A 234 SHEET 9 AA314 TYR B 452 THR B 458 -1 O LEU B 453 N SER B 426 SHEET 10 AA314 PRO B 396 CYS B 401 -1 N VAL B 399 O LEU B 454 SHEET 11 AA314 GLY B 371 ALA B 375 1 N VAL B 374 O TYR B 400 SHEET 12 AA314 LYS B 202 GLU B 207 1 N ILE B 204 O ILE B 373 SHEET 13 AA314 SER B 226 TYR B 231 1 O SER B 226 N MET B 203 SHEET 14 AA314 LEU B 254 PRO B 258 1 O TYR B 255 N ILE B 227 SHEET 1 AA4 4 PHE A 265 PRO A 270 0 SHEET 2 AA4 4 SER A 226 VAL A 243 -1 N ASN A 239 O THR A 269 SHEET 3 AA4 4 VAL B 420 GLN B 434 -1 O TRP B 429 N LEU A 234 SHEET 4 AA4 4 HIS B 441 MET B 446 -1 O MET B 446 N LEU B 430 SHEET 1 AA5 5 PHE B 34 GLN B 38 0 SHEET 2 AA5 5 PHE B 25 LYS B 29 -1 N LEU B 28 O LYS B 35 SHEET 3 AA5 5 ILE B 158 VAL B 161 -1 O THR B 159 N LYS B 29 SHEET 4 AA5 5 THR B 64 VAL B 68 -1 N PHE B 66 O ILE B 158 SHEET 5 AA5 5 SER B 73 LEU B 74 -1 O LEU B 74 N GLU B 67 SHEET 1 AA6 2 LYS B 44 THR B 46 0 SHEET 2 AA6 2 TRP B 51 TYR B 53 -1 O PHE B 52 N VAL B 45 LINK O3' A N 57 P A1MA N 58 1555 1555 1.61 LINK O3' A N 57 P B1MA N 58 1555 1555 1.61 LINK O3'A1MA N 58 P A G N 59 1555 1555 1.61 LINK OP1 U N 8 NA NA N 101 1555 1555 2.19 LINK OP2 A N 9 NA NA N 101 1555 1555 2.17 LINK NA NA N 101 O HOH N 217 1555 1555 2.48 LINK NA NA N 101 O HOH N 239 1555 1555 2.17 LINK NA NA N 101 O HOH N 263 1555 1555 2.16 LINK NA NA N 101 O HOH N 269 1555 1555 2.13 CISPEP 1 MET A 1 SER A 2 0 2.87 CISPEP 2 SER A 110 GLY A 111 0 1.71 CISPEP 3 ALA A 126 PRO A 127 0 1.84 SITE 1 AC1 22 THR A 84 GLN A 85 LEU A 87 SER A 110 SITE 2 AC1 22 GLY A 111 THR A 112 GLY A 113 SER A 114 SITE 3 AC1 22 GLY A 115 SER A 116 VAL A 117 GLU A 135 SITE 4 AC1 22 PHE A 136 ARG A 140 GLN A 162 ASP A 163 SITE 5 AC1 22 VAL A 164 ASP A 181 PRO A 183 HOH A 424 SITE 6 AC1 22 HOH A 507 C N 56 SITE 1 AC2 6 U N 8 A N 9 HOH N 217 HOH N 239 SITE 2 AC2 6 HOH N 263 HOH N 269 CRYST1 136.770 136.770 177.160 90.00 90.00 90.00 P 43 21 2 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 0.007312 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007312 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005645 0.00000