HEADER TRANSFERASE 14-NOV-15 5ERG TITLE CRYSTAL STRUCTURE OF THE TWO-SUBUNIT TRNA M1A58 METHYLTRANSFERASE TITLE 2 TRM6-TRM61 IN COMPLEX WITH SAM COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA (ADENINE(58)-N(1))-METHYLTRANSFERASE NON-CATALYTIC COMPND 3 SUBUNIT TRM6; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: GENERAL CONTROL NON-DEREPRESSIBLE PROTEIN 10,PROTEIN GCD10, COMPND 6 TRNA(M1A58)-METHYLTRANSFERASE SUBUNIT TRM6,TRNA(M1A58)MTASE SUBUNIT COMPND 7 TRM6; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: TRNA (ADENINE(58)-N(1))-METHYLTRANSFERASE CATALYTIC SUBUNIT COMPND 11 TRM61; COMPND 12 CHAIN: B; COMPND 13 SYNONYM: GENERAL CONTROL NON-DEREPRESSIBLE PROTEIN 14,PROTEIN GCD14, COMPND 14 TRNA(M1A58)-METHYLTRANSFERASE SUBUNIT TRM61,TRNA(M1A58)MTASE SUBUNIT COMPND 15 TRM61; COMPND 16 EC: 2.1.1.220; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 3 S288C); SOURCE 4 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 5 ORGANISM_TAXID: 559292; SOURCE 6 STRAIN: ATCC 204508 / S288C; SOURCE 7 GENE: GCD10, TIF33, TRM6, YNL062C, N2422; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 12 S288C); SOURCE 13 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 14 ORGANISM_TAXID: 559292; SOURCE 15 STRAIN: ATCC 204508 / S288C; SOURCE 16 GENE: GCD14, TRM61, YJL125C, J0710; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRNA, COMPLEX, SAM, METHYLATION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHU,M.WANG,C.WANG,X.FAN,X.JIANG,M.TENG,X.LI REVDAT 2 20-MAR-24 5ERG 1 REMARK REVDAT 1 14-SEP-16 5ERG 0 JRNL AUTH M.WANG,Y.ZHU,C.WANG,X.FAN,X.JIANG,M.EBRAHIMI,Z.QIAO,L.NIU, JRNL AUTH 2 M.TENG,X.LI JRNL TITL CRYSTAL STRUCTURE OF THE TWO-SUBUNIT TRNA M(1)A58 JRNL TITL 2 METHYLTRANSFERASE TRM6-TRM61 FROM SACCHAROMYCES CEREVISIAE. JRNL REF SCI REP V. 6 32562 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 27582183 JRNL DOI 10.1038/SREP32562 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 59326 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 2912 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 47.5916 - 6.0702 0.99 2848 125 0.1766 0.1725 REMARK 3 2 6.0702 - 4.8196 1.00 2758 127 0.1697 0.1878 REMARK 3 3 4.8196 - 4.2108 1.00 2735 143 0.1395 0.1686 REMARK 3 4 4.2108 - 3.8260 1.00 2695 145 0.1570 0.1831 REMARK 3 5 3.8260 - 3.5518 1.00 2671 156 0.1773 0.2024 REMARK 3 6 3.5518 - 3.3425 1.00 2704 119 0.1814 0.2142 REMARK 3 7 3.3425 - 3.1751 1.00 2677 161 0.1982 0.2497 REMARK 3 8 3.1751 - 3.0369 1.00 2697 123 0.1927 0.2368 REMARK 3 9 3.0369 - 2.9200 1.00 2707 127 0.2052 0.2655 REMARK 3 10 2.9200 - 2.8193 1.00 2677 138 0.1993 0.2420 REMARK 3 11 2.8193 - 2.7311 1.00 2682 124 0.2046 0.2279 REMARK 3 12 2.7311 - 2.6531 1.00 2646 156 0.2029 0.2590 REMARK 3 13 2.6531 - 2.5832 1.00 2657 143 0.2022 0.2330 REMARK 3 14 2.5832 - 2.5202 1.00 2658 158 0.2045 0.2343 REMARK 3 15 2.5202 - 2.4629 1.00 2685 121 0.2075 0.2667 REMARK 3 16 2.4629 - 2.4105 1.00 2663 116 0.2134 0.2229 REMARK 3 17 2.4105 - 2.3623 1.00 2638 167 0.2219 0.2809 REMARK 3 18 2.3623 - 2.3177 1.00 2646 154 0.2251 0.2636 REMARK 3 19 2.3177 - 2.2763 1.00 2660 149 0.2509 0.2994 REMARK 3 20 2.2763 - 2.2377 1.00 2631 151 0.3025 0.3812 REMARK 3 21 2.2377 - 2.2017 1.00 2679 109 0.2801 0.2551 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.910 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 : 0.009 5483 REMARK 3 ANGLE : 1.120 7416 REMARK 3 CHIRALITY : 0.053 815 REMARK 3 PLANARITY : 0.005 942 REMARK 3 DIHEDRAL : 15.309 2025 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 5ERG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-NOV-15. REMARK 100 THE DEPOSITION ID IS D_1000215186. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59358 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, PH 7.5, 2% V/V(+/-)-2 REMARK 280 -METHYL-2,4-PENTANEDIOL, 10% W/V POLYETHYLENE GLYCOL 6000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 68.98133 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 34.49067 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 34.49067 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 68.98133 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 19010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 56070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -71.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -68.98133 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 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 GLY A 61 REMARK 465 GLU A 62 REMARK 465 GLU A 63 REMARK 465 VAL A 64 REMARK 465 SER A 65 REMARK 465 SER A 66 REMARK 465 ASP A 67 REMARK 465 GLU A 68 REMARK 465 ASN A 69 REMARK 465 ARG A 70 REMARK 465 ASP A 71 REMARK 465 SER A 72 REMARK 465 LYS A 73 REMARK 465 PRO A 74 REMARK 465 LYS A 75 REMARK 465 ASN A 76 REMARK 465 LYS A 77 REMARK 465 ILE A 78 REMARK 465 GLN A 88 REMARK 465 GLU A 89 REMARK 465 ILE A 90 REMARK 465 LYS A 91 REMARK 465 ASP A 92 REMARK 465 VAL A 93 REMARK 465 ASN A 94 REMARK 465 ASN A 95 REMARK 465 ASP A 96 REMARK 465 LYS A 97 REMARK 465 ASP A 98 REMARK 465 ASP A 99 REMARK 465 GLY A 100 REMARK 465 GLN A 101 REMARK 465 SER A 102 REMARK 465 GLU A 103 REMARK 465 PRO A 104 REMARK 465 PRO A 105 REMARK 465 LEU A 106 REMARK 465 SER A 107 REMARK 465 ILE A 108 REMARK 465 LYS A 109 REMARK 465 GLU A 110 REMARK 465 LYS A 111 REMARK 465 SER A 112 REMARK 465 VAL A 113 REMARK 465 SER A 114 REMARK 465 LEU A 115 REMARK 465 GLU A 116 REMARK 465 LEU A 117 REMARK 465 SER A 118 REMARK 465 SER A 119 REMARK 465 ILE A 120 REMARK 465 ASP A 121 REMARK 465 SER A 122 REMARK 465 SER A 123 REMARK 465 ALA A 124 REMARK 465 THR A 125 REMARK 465 ASN A 126 REMARK 465 GLN A 127 REMARK 465 ASN A 128 REMARK 465 LEU A 129 REMARK 465 VAL A 130 REMARK 465 ASN A 131 REMARK 465 MET A 132 REMARK 465 GLY A 133 REMARK 465 SER A 134 REMARK 465 LYS A 135 REMARK 465 ALA A 136 REMARK 465 GLN A 137 REMARK 465 GLU A 138 REMARK 465 LEU A 139 REMARK 465 THR A 140 REMARK 465 VAL A 141 REMARK 465 GLU A 142 REMARK 465 GLU A 143 REMARK 465 ILE A 144 REMARK 465 GLU A 145 REMARK 465 LYS A 146 REMARK 465 MET A 147 REMARK 465 LYS A 148 REMARK 465 GLN A 149 REMARK 465 GLU A 150 REMARK 465 SER A 151 REMARK 465 LEU A 152 REMARK 465 SER A 153 REMARK 465 SER A 154 REMARK 465 LYS A 155 REMARK 465 GLU A 156 REMARK 465 ILE A 157 REMARK 465 ILE A 158 REMARK 465 ASP A 159 REMARK 465 LYS A 160 REMARK 465 ILE A 161 REMARK 465 ILE A 162 REMARK 465 LYS A 163 REMARK 465 SER A 164 REMARK 465 HIS A 165 REMARK 465 LYS A 166 REMARK 465 SER A 167 REMARK 465 PHE A 168 REMARK 465 HIS A 169 REMARK 465 ASN A 170 REMARK 465 LYS A 171 REMARK 465 THR A 172 REMARK 465 VAL A 173 REMARK 465 TYR A 174 REMARK 465 SER A 175 REMARK 465 GLN A 176 REMARK 465 GLU A 177 REMARK 465 LYS A 178 REMARK 465 TYR A 179 REMARK 465 VAL A 180 REMARK 465 ASN A 181 REMARK 465 ARG A 182 REMARK 465 LYS A 183 REMARK 465 LYS A 184 REMARK 465 GLN A 185 REMARK 465 LYS A 186 REMARK 465 PHE A 187 REMARK 465 ALA A 188 REMARK 465 GLU A 453 REMARK 465 PRO A 454 REMARK 465 VAL A 455 REMARK 465 SER A 456 REMARK 465 GLU A 457 REMARK 465 ASN A 458 REMARK 465 ALA A 459 REMARK 465 THR A 460 REMARK 465 ALA A 461 REMARK 465 ALA A 462 REMARK 465 ASP A 463 REMARK 465 SER A 464 REMARK 465 SER A 465 REMARK 465 GLU A 466 REMARK 465 LYS A 467 REMARK 465 LEU A 468 REMARK 465 ALA A 469 REMARK 465 GLU A 470 REMARK 465 HIS A 471 REMARK 465 GLY A 472 REMARK 465 ALA A 473 REMARK 465 LYS A 474 REMARK 465 LYS A 475 REMARK 465 GLN A 476 REMARK 465 LYS A 477 REMARK 465 ILE A 478 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 THR B 3 REMARK 465 LYS B 65 REMARK 465 GLY B 66 REMARK 465 SER B 67 REMARK 465 ASN B 68 REMARK 465 LYS B 69 REMARK 465 LEU B 286 REMARK 465 GLN B 287 REMARK 465 GLY B 288 REMARK 465 VAL B 289 REMARK 465 GLU B 290 REMARK 465 ARG B 291 REMARK 465 ARG B 292 REMARK 465 LYS B 293 REMARK 465 ARG B 294 REMARK 465 MET B 295 REMARK 465 PHE B 296 REMARK 465 ASN B 297 REMARK 465 ASN B 298 REMARK 465 THR B 299 REMARK 465 ILE B 300 REMARK 465 ASP B 301 REMARK 465 SER B 302 REMARK 465 ASN B 303 REMARK 465 ASP B 304 REMARK 465 GLU B 305 REMARK 465 LYS B 306 REMARK 465 VAL B 307 REMARK 465 GLY B 308 REMARK 465 LYS B 309 REMARK 465 ARG B 310 REMARK 465 ASN B 311 REMARK 465 GLU B 312 REMARK 465 ASP B 313 REMARK 465 GLY B 314 REMARK 465 VAL B 315 REMARK 465 PRO B 316 REMARK 465 LEU B 317 REMARK 465 THR B 318 REMARK 465 GLU B 319 REMARK 465 LYS B 320 REMARK 465 ALA B 321 REMARK 465 LYS B 322 REMARK 465 PHE B 323 REMARK 465 ASN B 324 REMARK 465 PRO B 325 REMARK 465 PHE B 326 REMARK 465 GLY B 327 REMARK 465 LYS B 328 REMARK 465 GLY B 329 REMARK 465 SER B 330 REMARK 465 ARG B 331 REMARK 465 ARG B 379 REMARK 465 SER B 380 REMARK 465 THR B 381 REMARK 465 GLU B 382 REMARK 465 LYS B 383 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 HIS A -6 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 28 CE NZ REMARK 470 ASP A 280 OD1 OD2 REMARK 470 LYS A 283 CG CD CE NZ REMARK 470 GLU A 289 CG CD OE1 OE2 REMARK 470 GLU A 294 CG CD OE1 OE2 REMARK 470 LEU A 310 CD1 CD2 REMARK 470 GLN A 311 CG CD OE1 NE2 REMARK 470 ARG A 316 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 323 CG CD OE1 OE2 REMARK 470 GLU A 324 CG CD OE1 OE2 REMARK 470 ARG A 326 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 332 CG CD CE NZ REMARK 470 LYS A 333 CE NZ REMARK 470 ASN A 334 OD1 ND2 REMARK 470 GLU A 355 CG CD OE1 OE2 REMARK 470 LYS A 379 CE NZ REMARK 470 LYS A 428 CG CD CE NZ REMARK 470 ASN B 4 CG OD1 ND2 REMARK 470 THR B 41 OG1 CG2 REMARK 470 ARG B 63 CG CD NE CZ NH1 NH2 REMARK 470 THR B 64 OG1 CG2 REMARK 470 HIS B 89 CG ND1 CD2 CE1 NE2 REMARK 470 ARG B 90 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 171 CD OE1 NE2 REMARK 470 ILE B 332 CG1 CG2 CD1 REMARK 470 LYS B 333 CD CE NZ REMARK 470 LYS B 340 CD CE NZ REMARK 470 LYS B 352 NZ REMARK 470 GLU B 376 CG CD OE1 OE2 REMARK 470 LEU B 378 CG CD1 CD2 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 OD1 ASP B 280 NH2 ARG B 283 2.06 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 LYS A 20 -2.07 74.13 REMARK 500 LYS A 428 51.79 -155.26 REMARK 500 ASP B 11 -61.02 -95.51 REMARK 500 ASP B 160 -88.78 -116.07 REMARK 500 ASN B 161 25.01 -140.07 REMARK 500 HIS B 284 -8.61 -56.19 REMARK 500 ASP B 336 118.84 -39.01 REMARK 500 GLU B 376 14.53 -69.75 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 SAM B 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5EQJ RELATED DB: PDB DBREF 5ERG A 1 478 UNP P41814 TRM6_YEAST 1 478 DBREF 5ERG B 1 383 UNP P46959 TRM61_YEAST 1 383 SEQADV 5ERG HIS A -9 UNP P41814 EXPRESSION TAG SEQADV 5ERG HIS A -8 UNP P41814 EXPRESSION TAG SEQADV 5ERG HIS A -7 UNP P41814 EXPRESSION TAG SEQADV 5ERG HIS A -6 UNP P41814 EXPRESSION TAG SEQADV 5ERG HIS A -5 UNP P41814 EXPRESSION TAG SEQADV 5ERG HIS A -4 UNP P41814 EXPRESSION TAG SEQADV 5ERG SER A -3 UNP P41814 EXPRESSION TAG SEQADV 5ERG GLN A -2 UNP P41814 EXPRESSION TAG SEQADV 5ERG ASP A -1 UNP P41814 EXPRESSION TAG SEQADV 5ERG PRO A 0 UNP P41814 EXPRESSION TAG SEQRES 1 A 488 HIS HIS HIS HIS HIS HIS SER GLN ASP PRO MET ASN ALA SEQRES 2 A 488 LEU THR THR ILE ASP PHE ASN GLN HIS VAL ILE VAL ARG SEQRES 3 A 488 LEU PRO SER LYS ASN TYR LYS ILE VAL GLU LEU LYS PRO SEQRES 4 A 488 ASN THR SER VAL SER LEU GLY LYS PHE GLY ALA PHE GLU SEQRES 5 A 488 VAL ASN ASP ILE ILE GLY TYR PRO PHE GLY LEU THR PHE SEQRES 6 A 488 GLU ILE TYR TYR ASP GLY GLU GLU VAL SER SER ASP GLU SEQRES 7 A 488 ASN ARG ASP SER LYS PRO LYS ASN LYS ILE PRO ILE GLY SEQRES 8 A 488 LYS VAL ARG LEU LEU SER GLN GLU ILE LYS ASP VAL ASN SEQRES 9 A 488 ASN ASP LYS ASP ASP GLY GLN SER GLU PRO PRO LEU SER SEQRES 10 A 488 ILE LYS GLU LYS SER VAL SER LEU GLU LEU SER SER ILE SEQRES 11 A 488 ASP SER SER ALA THR ASN GLN ASN LEU VAL ASN MET GLY SEQRES 12 A 488 SER LYS ALA GLN GLU LEU THR VAL GLU GLU ILE GLU LYS SEQRES 13 A 488 MET LYS GLN GLU SER LEU SER SER LYS GLU ILE ILE ASP SEQRES 14 A 488 LYS ILE ILE LYS SER HIS LYS SER PHE HIS ASN LYS THR SEQRES 15 A 488 VAL TYR SER GLN GLU LYS TYR VAL ASN ARG LYS LYS GLN SEQRES 16 A 488 LYS PHE ALA LYS TYR PHE THR VAL GLU TYR LEU SER SER SEQRES 17 A 488 SER ASN LEU LEU GLN PHE LEU ILE ASP LYS GLY ASP ILE SEQRES 18 A 488 GLN ARG VAL LEU ASP MET SER GLN GLU SER MET GLY MET SEQRES 19 A 488 LEU LEU ASN LEU ALA ASN ILE GLN SER GLU GLY ASN TYR SEQRES 20 A 488 LEU CYS MET ASP GLU THR GLY GLY LEU LEU VAL TYR PHE SEQRES 21 A 488 LEU LEU GLU ARG MET PHE GLY GLY ASP ASN GLU SER LYS SEQRES 22 A 488 SER LYS GLY LYS VAL ILE VAL ILE HIS GLU ASN GLU HIS SEQRES 23 A 488 ALA ASN LEU ASP LEU LEU LYS PHE ALA ASN TYR SER GLU SEQRES 24 A 488 LYS PHE ILE LYS GLU HIS VAL HIS THR ILE SER LEU LEU SEQRES 25 A 488 ASP PHE PHE GLU PRO PRO THR LEU GLN GLU ILE GLN SER SEQRES 26 A 488 ARG PHE THR PRO LEU PRO LYS GLU GLU ALA ARG ALA LEU SEQRES 27 A 488 LYS GLY GLY LYS LYS ASN SER TYR TYR ARG LYS LEU ARG SEQRES 28 A 488 TRP TYR ASN THR GLN TRP GLN ILE LEU GLU LEU THR GLY SEQRES 29 A 488 GLU PHE LEU TYR ASP GLY LEU VAL MET ALA THR THR LEU SEQRES 30 A 488 HIS LEU PRO THR LEU VAL PRO LYS LEU ALA GLU LYS ILE SEQRES 31 A 488 HIS GLY SER ARG PRO ILE VAL CYS TYR GLY GLN PHE LYS SEQRES 32 A 488 GLU THR LEU LEU GLU LEU ALA HIS THR LEU TYR SER ASP SEQRES 33 A 488 LEU ARG PHE LEU ALA PRO SER ILE LEU GLU THR ARG CYS SEQRES 34 A 488 ARG PRO TYR GLN SER ILE ARG GLY LYS LEU HIS PRO LEU SEQRES 35 A 488 MET THR MET LYS GLY GLY GLY GLY TYR LEU MET TRP CYS SEQRES 36 A 488 HIS ARG VAL ILE PRO ALA PRO GLU PRO VAL SER GLU ASN SEQRES 37 A 488 ALA THR ALA ALA ASP SER SER GLU LYS LEU ALA GLU HIS SEQRES 38 A 488 GLY ALA LYS LYS GLN LYS ILE SEQRES 1 B 383 MET SER THR ASN CYS PHE SER GLY TYR LYS ASP LEU ILE SEQRES 2 B 383 LYS GLU GLY ASP LEU THR LEU ILE TRP VAL SER ARG ASP SEQRES 3 B 383 ASN ILE LYS PRO VAL ARG MET HIS SER GLU GLU VAL PHE SEQRES 4 B 383 ASN THR ARG TYR GLY SER PHE PRO HIS LYS ASP ILE ILE SEQRES 5 B 383 GLY LYS PRO TYR GLY SER GLN ILE ALA ILE ARG THR LYS SEQRES 6 B 383 GLY SER ASN LYS PHE ALA PHE VAL HIS VAL LEU GLN PRO SEQRES 7 B 383 THR PRO GLU LEU TRP THR LEU SER LEU PRO HIS ARG THR SEQRES 8 B 383 GLN ILE VAL TYR THR PRO ASP SER SER TYR ILE MET GLN SEQRES 9 B 383 ARG LEU ASN CYS SER PRO HIS SER ARG VAL ILE GLU ALA SEQRES 10 B 383 GLY THR GLY SER GLY SER PHE SER HIS ALA PHE ALA ARG SEQRES 11 B 383 SER VAL GLY HIS LEU PHE SER PHE GLU PHE HIS HIS ILE SEQRES 12 B 383 ARG TYR GLU GLN ALA LEU GLU GLU PHE LYS GLU HIS GLY SEQRES 13 B 383 LEU ILE ASP ASP ASN VAL THR ILE THR HIS ARG ASP VAL SEQRES 14 B 383 CYS GLN GLY GLY PHE LEU ILE LYS LYS GLY ASP THR THR SEQRES 15 B 383 SER TYR GLU PHE GLY ASN ASN GLU THR ALA ALA SER LEU SEQRES 16 B 383 ASN ALA ASN VAL VAL PHE LEU ASP LEU PRO ALA PRO TRP SEQRES 17 B 383 ASP ALA ILE PRO HIS LEU ASP SER VAL ILE SER VAL ASP SEQRES 18 B 383 GLU LYS VAL GLY LEU CYS CYS PHE SER PRO CYS ILE GLU SEQRES 19 B 383 GLN VAL ASP LYS THR LEU ASP VAL LEU GLU LYS TYR GLY SEQRES 20 B 383 TRP THR ASP VAL GLU MET VAL GLU ILE GLN GLY ARG GLN SEQRES 21 B 383 TYR GLU SER ARG ARG GLN MET VAL ARG SER LEU ASN ASP SEQRES 22 B 383 ALA LEU GLU ARG LEU ARG ASP ILE LYS ARG HIS LYS LEU SEQRES 23 B 383 GLN GLY VAL GLU ARG ARG LYS ARG MET PHE ASN ASN THR SEQRES 24 B 383 ILE ASP SER ASN ASP GLU LYS VAL GLY LYS ARG ASN GLU SEQRES 25 B 383 ASP GLY VAL PRO LEU THR GLU LYS ALA LYS PHE ASN PRO SEQRES 26 B 383 PHE GLY LYS GLY SER ARG ILE LYS GLU GLY ASP SER ASN SEQRES 27 B 383 TYR LYS TRP LYS GLU VAL THR LYS MET GLU ALA GLU ILE SEQRES 28 B 383 LYS SER HIS THR SER TYR LEU THR PHE ALA PHE LYS VAL SEQRES 29 B 383 VAL ASN ARG SER ARG ASP ASP GLU LYS VAL ASN GLU ILE SEQRES 30 B 383 LEU ARG SER THR GLU LYS HET SAM B 401 27 HETNAM SAM S-ADENOSYLMETHIONINE FORMUL 3 SAM C15 H22 N6 O5 S FORMUL 4 HOH *199(H2 O) HELIX 1 AA1 GLY A 36 PHE A 38 5 3 HELIX 2 AA2 ASN A 44 ILE A 46 5 3 HELIX 3 AA3 SER A 197 LYS A 208 1 12 HELIX 4 AA4 SER A 218 ALA A 229 1 12 HELIX 5 AA5 GLY A 245 GLY A 257 1 13 HELIX 6 AA6 LEU A 279 ALA A 285 5 7 HELIX 7 AA7 SER A 288 HIS A 295 1 8 HELIX 8 AA8 LEU A 301 GLU A 306 1 6 HELIX 9 AA9 THR A 309 SER A 315 1 7 HELIX 10 AB1 PRO A 321 LEU A 328 1 8 HELIX 11 AB2 LYS A 329 GLY A 354 1 26 HELIX 12 AB3 HIS A 368 THR A 371 5 4 HELIX 13 AB4 LEU A 372 ALA A 377 1 6 HELIX 14 AB5 GLU A 378 ILE A 380 5 3 HELIX 15 AB6 PHE A 392 SER A 405 1 14 HELIX 16 AB7 LYS B 49 ILE B 51 5 3 HELIX 17 AB8 THR B 79 LEU B 87 1 9 HELIX 18 AB9 TYR B 95 LEU B 106 1 12 HELIX 19 AC1 GLY B 122 VAL B 132 1 11 HELIX 20 AC2 HIS B 141 HIS B 155 1 15 HELIX 21 AC3 ASP B 168 GLY B 173 1 6 HELIX 22 AC4 ALA B 206 VAL B 217 5 12 HELIX 23 AC5 CYS B 232 TYR B 246 1 15 HELIX 24 AC6 SER B 270 HIS B 284 1 15 HELIX 25 AC7 ASP B 370 GLU B 376 1 7 SHEET 1 AA1 5 TYR A 22 GLU A 26 0 SHEET 2 AA1 5 HIS A 12 ARG A 16 -1 N VAL A 15 O LYS A 23 SHEET 3 AA1 5 TYR A 190 GLU A 194 -1 O THR A 192 N ARG A 16 SHEET 4 AA1 5 THR A 54 TYR A 58 -1 N PHE A 55 O PHE A 191 SHEET 5 AA1 5 LYS A 82 LEU A 85 -1 O ARG A 84 N GLU A 56 SHEET 1 AA2 2 SER A 32 SER A 34 0 SHEET 2 AA2 2 ALA A 40 GLU A 42 -1 O PHE A 41 N VAL A 33 SHEET 1 AA314 VAL A 296 SER A 300 0 SHEET 2 AA314 LYS A 267 HIS A 272 1 N VAL A 270 O HIS A 297 SHEET 3 AA314 ASN A 236 ASP A 241 1 N TYR A 237 O ILE A 269 SHEET 4 AA314 LEU A 361 ALA A 364 1 O VAL A 362 N LEU A 238 SHEET 5 AA314 PRO A 385 GLY A 390 1 O TYR A 389 N MET A 363 SHEET 6 AA314 TYR A 441 ARG A 447 -1 O TYR A 441 N GLY A 390 SHEET 7 AA314 PHE A 409 GLN A 423 -1 N LEU A 415 O LEU A 442 SHEET 8 AA314 THR B 249 MET B 267 -1 O MET B 253 N TYR A 422 SHEET 9 AA314 TYR B 357 LYS B 363 -1 O PHE B 362 N THR B 249 SHEET 10 AA314 VAL B 224 SER B 230 -1 N SER B 230 O TYR B 357 SHEET 11 AA314 VAL B 199 LEU B 202 1 N LEU B 202 O PHE B 229 SHEET 12 AA314 ARG B 113 ALA B 117 1 N ILE B 115 O PHE B 201 SHEET 13 AA314 HIS B 134 GLU B 139 1 O PHE B 136 N VAL B 114 SHEET 14 AA314 VAL B 162 HIS B 166 1 O THR B 163 N SER B 137 SHEET 1 AA4 4 HIS A 430 PRO A 431 0 SHEET 2 AA4 4 PHE A 409 GLN A 423 -1 N GLN A 423 O HIS A 430 SHEET 3 AA4 4 THR B 249 MET B 267 -1 O MET B 253 N TYR A 422 SHEET 4 AA4 4 TRP B 341 MET B 347 -1 O VAL B 344 N ARG B 264 SHEET 1 AA5 4 ASN B 27 ARG B 32 0 SHEET 2 AA5 4 LEU B 18 SER B 24 -1 N ILE B 21 O LYS B 29 SHEET 3 AA5 4 ALA B 71 LEU B 76 -1 O LEU B 76 N LEU B 20 SHEET 4 AA5 4 SER B 58 ILE B 62 -1 N ILE B 60 O VAL B 73 SHEET 1 AA6 2 VAL B 38 THR B 41 0 SHEET 2 AA6 2 GLY B 44 PRO B 47 -1 O PHE B 46 N PHE B 39 CISPEP 1 ALA B 117 GLY B 118 0 -1.91 SITE 1 AC1 19 GLN B 92 VAL B 94 GLY B 118 THR B 119 SITE 2 AC1 19 GLY B 120 SER B 121 GLY B 122 SER B 123 SITE 3 AC1 19 PHE B 124 GLU B 139 PHE B 140 ARG B 144 SITE 4 AC1 19 ARG B 167 ASP B 168 VAL B 169 CYS B 170 SITE 5 AC1 19 ASP B 203 LEU B 204 HOH B 506 CRYST1 139.916 139.916 103.472 90.00 90.00 120.00 P 32 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 0.007147 0.004126 0.000000 0.00000 SCALE2 0.000000 0.008253 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009664 0.00000