HEADER TRANSFERASE/TRANSFERASE INHIBITOR 23-AUG-21 7RXV TITLE HUMAN METHIONINE ADENOSYLTRANSFERASE 2A BOUND TO METHYLTHIOADENOSINE, TITLE 2 MALONATE (MLA) AND MGF3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ADOMET SYNTHASE 2,METHIONINE ADENOSYLTRANSFERASE 2,MAT 2, COMPND 5 METHIONINE ADENOSYLTRANSFERASE II,MAT-II; COMPND 6 EC: 2.5.1.6; COMPND 7 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: MAT2A, AMS2, MATA2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS SAM SYNTHETASE, ENZYME MECHANISM, INHIBITOR, TRANSITION STATE, KEYWDS 2 TRANSFERASE-INHIBITOR COMPLEX, TRANSFERASE, TRANSFERASE-TRANSFERASE KEYWDS 3 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.FEDOROV,C.N.NILAND,V.L.SCHRAMM,A.GHOSH REVDAT 3 18-OCT-23 7RXV 1 REMARK REVDAT 2 17-NOV-21 7RXV 1 JRNL REVDAT 1 03-NOV-21 7RXV 0 JRNL AUTH A.GHOSH,C.N.NILAND,S.M.CAHILL,N.M.KARADKHELKAR,V.L.SCHRAMM JRNL TITL MECHANISM OF TRIPHOSPHATE HYDROLYSIS BY HUMAN MAT2A AT 1.07 JRNL TITL 2 ANGSTROM RESOLUTION. JRNL REF J.AM.CHEM.SOC. V. 143 18325 2021 JRNL REFN ESSN 1520-5126 JRNL PMID 34668717 JRNL DOI 10.1021/JACS.1C09328 REMARK 2 REMARK 2 RESOLUTION. 1.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19RC5_4047 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) : 1.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 3 NUMBER OF REFLECTIONS : 153623 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.130 REMARK 3 R VALUE (WORKING SET) : 0.130 REMARK 3 FREE R VALUE : 0.139 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 7718 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 19.8600 - 3.3200 1.00 5488 291 0.1256 0.1386 REMARK 3 2 3.3200 - 2.6400 1.00 5288 311 0.1301 0.1300 REMARK 3 3 2.6400 - 2.3000 1.00 5306 247 0.1235 0.1408 REMARK 3 4 2.3000 - 2.0900 1.00 5281 281 0.1217 0.1238 REMARK 3 5 2.0900 - 1.9400 1.00 5262 268 0.1214 0.1254 REMARK 3 6 1.9400 - 1.8300 1.00 5188 300 0.1269 0.1276 REMARK 3 7 1.8300 - 1.7400 1.00 5235 276 0.1265 0.1413 REMARK 3 8 1.7400 - 1.6600 1.00 5221 277 0.1235 0.1332 REMARK 3 9 1.6600 - 1.6000 1.00 5199 294 0.1201 0.1403 REMARK 3 10 1.6000 - 1.5400 1.00 5205 272 0.1194 0.1259 REMARK 3 11 1.5400 - 1.4900 1.00 5187 272 0.1231 0.1325 REMARK 3 12 1.4900 - 1.4500 1.00 5242 244 0.1233 0.1361 REMARK 3 13 1.4500 - 1.4100 1.00 5199 270 0.1293 0.1465 REMARK 3 14 1.4100 - 1.3800 1.00 5182 305 0.1270 0.1385 REMARK 3 15 1.3800 - 1.3500 1.00 5165 303 0.1289 0.1409 REMARK 3 16 1.3500 - 1.3200 1.00 5170 274 0.1337 0.1417 REMARK 3 17 1.3200 - 1.2900 1.00 5195 255 0.1315 0.1428 REMARK 3 18 1.2900 - 1.2700 1.00 5181 285 0.1316 0.1319 REMARK 3 19 1.2700 - 1.2500 1.00 5243 245 0.1331 0.1430 REMARK 3 20 1.2500 - 1.2200 1.00 5173 280 0.1329 0.1666 REMARK 3 21 1.2200 - 1.2100 1.00 5174 264 0.1374 0.1499 REMARK 3 22 1.2100 - 1.1900 0.99 5103 286 0.1447 0.1534 REMARK 3 23 1.1900 - 1.1700 0.94 4879 268 0.1493 0.1630 REMARK 3 24 1.1700 - 1.1500 0.91 4694 244 0.1545 0.1643 REMARK 3 25 1.1500 - 1.1400 0.86 4460 224 0.1613 0.1840 REMARK 3 26 1.1400 - 1.1200 0.80 4154 210 0.1685 0.1777 REMARK 3 27 1.1200 - 1.1100 0.72 3760 188 0.1770 0.1755 REMARK 3 28 1.1100 - 1.0900 0.66 3388 192 0.1900 0.2092 REMARK 3 29 1.0900 - 1.0800 0.59 3071 149 0.2140 0.2130 REMARK 3 30 1.0800 - 1.0700 0.50 2612 143 0.2365 0.2320 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) : 0.060 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.23 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 16:18 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.203 -12.108 -47.858 REMARK 3 T TENSOR REMARK 3 T11: 0.2313 T22: 0.2201 REMARK 3 T33: 0.1015 T12: 0.0030 REMARK 3 T13: 0.0305 T23: -0.0205 REMARK 3 L TENSOR REMARK 3 L11: 3.3475 L22: 6.2627 REMARK 3 L33: 9.1864 L12: 4.2038 REMARK 3 L13: 1.5185 L23: -0.9827 REMARK 3 S TENSOR REMARK 3 S11: 0.1114 S12: 1.4425 S13: -0.3666 REMARK 3 S21: -1.2807 S22: -0.1928 S23: -0.3883 REMARK 3 S31: 0.2570 S32: 0.1037 S33: 0.0507 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 19:80 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.131 -4.729 -13.534 REMARK 3 T TENSOR REMARK 3 T11: 0.0756 T22: 0.0869 REMARK 3 T33: 0.0849 T12: 0.0028 REMARK 3 T13: 0.0022 T23: 0.0057 REMARK 3 L TENSOR REMARK 3 L11: 0.3179 L22: 0.3839 REMARK 3 L33: 0.5269 L12: -0.1118 REMARK 3 L13: -0.1604 L23: 0.0893 REMARK 3 S TENSOR REMARK 3 S11: -0.0276 S12: -0.0409 S13: -0.0074 REMARK 3 S21: 0.0448 S22: 0.0262 S23: 0.0444 REMARK 3 S31: 0.0052 S32: -0.0423 S33: 0.0033 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 81:89 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.828 -14.120 -7.204 REMARK 3 T TENSOR REMARK 3 T11: 0.0688 T22: 0.1175 REMARK 3 T33: 0.0826 T12: -0.0168 REMARK 3 T13: 0.0103 T23: 0.0134 REMARK 3 L TENSOR REMARK 3 L11: 5.4016 L22: 5.4775 REMARK 3 L33: 6.8915 L12: -1.8876 REMARK 3 L13: -1.2947 L23: 2.6299 REMARK 3 S TENSOR REMARK 3 S11: -0.1021 S12: 0.1098 S13: -0.1547 REMARK 3 S21: -0.0017 S22: -0.0207 S23: 0.3449 REMARK 3 S31: 0.0958 S32: -0.4764 S33: 0.1556 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 90:176 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.326 -7.670 -20.130 REMARK 3 T TENSOR REMARK 3 T11: 0.0530 T22: 0.0861 REMARK 3 T33: 0.0924 T12: -0.0161 REMARK 3 T13: -0.0004 T23: -0.0002 REMARK 3 L TENSOR REMARK 3 L11: 0.0976 L22: 0.5582 REMARK 3 L33: 0.3888 L12: -0.1260 REMARK 3 L13: -0.0105 L23: 0.0122 REMARK 3 S TENSOR REMARK 3 S11: -0.0070 S12: -0.0074 S13: -0.0141 REMARK 3 S21: 0.0081 S22: 0.0041 S23: 0.0458 REMARK 3 S31: 0.0102 S32: -0.0402 S33: 0.0037 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN A AND RESID 177:192 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.856 -15.560 -36.189 REMARK 3 T TENSOR REMARK 3 T11: 0.0824 T22: 0.0404 REMARK 3 T33: 0.0800 T12: -0.0002 REMARK 3 T13: 0.0023 T23: -0.0196 REMARK 3 L TENSOR REMARK 3 L11: 1.6405 L22: 1.4480 REMARK 3 L33: 2.8279 L12: -0.0102 REMARK 3 L13: -0.3992 L23: -0.3212 REMARK 3 S TENSOR REMARK 3 S11: -0.0452 S12: 0.1597 S13: -0.0123 REMARK 3 S21: -0.1792 S22: -0.0496 S23: -0.0306 REMARK 3 S31: 0.0292 S32: 0.1202 S33: 0.0817 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN A AND RESID 193:296 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.389 -16.242 -27.150 REMARK 3 T TENSOR REMARK 3 T11: 0.0880 T22: 0.0832 REMARK 3 T33: 0.0893 T12: -0.0073 REMARK 3 T13: -0.0008 T23: -0.0047 REMARK 3 L TENSOR REMARK 3 L11: 0.4015 L22: 0.5542 REMARK 3 L33: 0.3118 L12: -0.2287 REMARK 3 L13: 0.0568 L23: -0.0509 REMARK 3 S TENSOR REMARK 3 S11: -0.0022 S12: 0.0122 S13: -0.0489 REMARK 3 S21: -0.0429 S22: 0.0140 S23: 0.0003 REMARK 3 S31: 0.0532 S32: 0.0146 S33: -0.0124 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN A AND RESID 297:395 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.808 -0.845 -36.246 REMARK 3 T TENSOR REMARK 3 T11: 0.0931 T22: 0.0862 REMARK 3 T33: 0.0870 T12: -0.0071 REMARK 3 T13: -0.0146 T23: -0.0042 REMARK 3 L TENSOR REMARK 3 L11: 0.4481 L22: 0.6012 REMARK 3 L33: 0.4012 L12: -0.1468 REMARK 3 L13: -0.0352 L23: -0.0037 REMARK 3 S TENSOR REMARK 3 S11: 0.0054 S12: 0.0551 S13: -0.0181 REMARK 3 S21: -0.1063 S22: 0.0009 S23: 0.0859 REMARK 3 S31: 0.0076 S32: -0.0636 S33: -0.0097 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 7RXV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-AUG-21. REMARK 100 THE DEPOSITION ID IS D_1000259193. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : KB MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 153643 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.070 REMARK 200 RESOLUTION RANGE LOW (A) : 19.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 52.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.57000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: 7L1A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4% TACSIMATE (1.83 M MALONIC ACID, REMARK 280 0.25 M AMMONIUM CITRATE TRIBASIC, 0.12 M SUCCINIC ACID, 0.3 M DL- REMARK 280 MALIC ACID, 0.4 M SODIUM ACETATE TRIHYDRATE, 0.5 M SODIUM REMARK 280 FORMATE, AND 0.16 M AMMONIUM TARTRATE DIBASIC) AND 12% PEG-3350, REMARK 280 PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 33.99050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.06100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 58.65750 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.99050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.06100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 58.65750 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.99050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.06100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 58.65750 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.99050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.06100 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 58.65750 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: 10140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 711 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 876 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 901 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 981 LIES ON A SPECIAL POSITION. 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 MET A -21 REMARK 465 HIS A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 SER A -14 REMARK 465 SER A -13 REMARK 465 GLY A -12 REMARK 465 VAL A -11 REMARK 465 ASP A -10 REMARK 465 LEU A -9 REMARK 465 GLY A -8 REMARK 465 THR A -7 REMARK 465 GLU A -6 REMARK 465 ASN A -5 REMARK 465 LEU A -4 REMARK 465 TYR A -3 REMARK 465 PHE A -2 REMARK 465 GLN A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 GLY A 3 REMARK 465 GLN A 4 REMARK 465 LEU A 5 REMARK 465 ASN A 6 REMARK 465 GLY A 7 REMARK 465 PHE A 8 REMARK 465 HIS A 9 REMARK 465 GLU A 10 REMARK 465 ALA A 11 REMARK 465 PHE A 12 REMARK 465 ILE A 13 REMARK 465 GLU A 14 REMARK 465 GLU A 15 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 HD22 ASN A 105 HD22 ASN A 105 3555 1.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PHE A 250 CB - CG - CD1 ANGL. DEV. = 4.3 DEGREES 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 VAL A 226 -66.41 -109.50 REMARK 500 THR A 270 -102.19 -122.70 REMARK 500 TYR A 335 17.25 59.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 981 DISTANCE = 5.85 ANGSTROMS 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 A 506 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 31 OD2 REMARK 620 2 MLA A 503 O1A 85.8 REMARK 620 3 MLA A 503 O3B 173.3 87.8 REMARK 620 4 HOH A 631 O 86.9 86.4 90.5 REMARK 620 5 HOH A 637 O 90.8 171.2 95.1 85.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 507 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 57 OE2 REMARK 620 2 ASP A 258 OD1 36.2 REMARK 620 3 ALA A 259 O 32.5 6.2 REMARK 620 4 MLA A 503 O3B 37.5 10.2 15.4 REMARK 620 5 HOH A 631 O 29.2 8.3 9.2 9.6 REMARK 620 6 HOH A 637 O 34.8 7.1 11.6 4.0 5.9 REMARK 620 7 HOH A 686 O 45.5 10.1 13.1 17.1 18.4 15.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 509 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 201 O REMARK 620 2 ASP A 239 O 96.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 508 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 324 O REMARK 620 2 HIS A 326 O 97.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MGF A 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 785 O REMARK 620 2 MGF A 504 F1 81.5 REMARK 620 3 MGF A 504 F2 80.5 119.9 REMARK 620 4 MGF A 504 F3 113.5 119.9 119.9 REMARK 620 N 1 2 3 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7L1A RELATED DB: PDB REMARK 900 HUMAN METHIONINE ADENOSYLTRANSFERASE 2A BOUND TO REMARK 900 METHYLTHIOADENOSINE AND INHIBITOR, DI-IMIDO TRIPHOSPHATE (PNPNP) REMARK 900 RELATED ID: 7RXW RELATED DB: PDB REMARK 900 HUMAN METHIONINE ADENOSYLTRANSFERASE 2A BOUND TO REMARK 900 METHYLTHIOADENOSINE AND INHIBITOR, IMIDO-DIPHOSPHATE (PNP) REMARK 900 RELATED ID: 7RXX RELATED DB: PDB REMARK 900 HUMAN METHIONINE ADENOSYLTRANSFERASE 2A BOUND TO REMARK 900 METHYLTHIOADENOSINE AND TWO SULFATE IONS DBREF 7RXV A 1 395 UNP P31153 METK2_HUMAN 1 395 SEQADV 7RXV MET A -21 UNP P31153 EXPRESSION TAG SEQADV 7RXV HIS A -20 UNP P31153 EXPRESSION TAG SEQADV 7RXV HIS A -19 UNP P31153 EXPRESSION TAG SEQADV 7RXV HIS A -18 UNP P31153 EXPRESSION TAG SEQADV 7RXV HIS A -17 UNP P31153 EXPRESSION TAG SEQADV 7RXV HIS A -16 UNP P31153 EXPRESSION TAG SEQADV 7RXV HIS A -15 UNP P31153 EXPRESSION TAG SEQADV 7RXV SER A -14 UNP P31153 EXPRESSION TAG SEQADV 7RXV SER A -13 UNP P31153 EXPRESSION TAG SEQADV 7RXV GLY A -12 UNP P31153 EXPRESSION TAG SEQADV 7RXV VAL A -11 UNP P31153 EXPRESSION TAG SEQADV 7RXV ASP A -10 UNP P31153 EXPRESSION TAG SEQADV 7RXV LEU A -9 UNP P31153 EXPRESSION TAG SEQADV 7RXV GLY A -8 UNP P31153 EXPRESSION TAG SEQADV 7RXV THR A -7 UNP P31153 EXPRESSION TAG SEQADV 7RXV GLU A -6 UNP P31153 EXPRESSION TAG SEQADV 7RXV ASN A -5 UNP P31153 EXPRESSION TAG SEQADV 7RXV LEU A -4 UNP P31153 EXPRESSION TAG SEQADV 7RXV TYR A -3 UNP P31153 EXPRESSION TAG SEQADV 7RXV PHE A -2 UNP P31153 EXPRESSION TAG SEQADV 7RXV GLN A -1 UNP P31153 EXPRESSION TAG SEQADV 7RXV SER A 0 UNP P31153 EXPRESSION TAG SEQRES 1 A 417 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 417 GLY THR GLU ASN LEU TYR PHE GLN SER MET ASN GLY GLN SEQRES 3 A 417 LEU ASN GLY PHE HIS GLU ALA PHE ILE GLU GLU GLY THR SEQRES 4 A 417 PHE LEU PHE THR SER GLU SER VAL GLY GLU GLY HIS PRO SEQRES 5 A 417 ASP LYS ILE CYS ASP GLN ILE SER ASP ALA VAL LEU ASP SEQRES 6 A 417 ALA HIS LEU GLN GLN ASP PRO ASP ALA LYS VAL ALA CYS SEQRES 7 A 417 GLU THR VAL ALA LYS THR GLY MET ILE LEU LEU ALA GLY SEQRES 8 A 417 GLU ILE THR SER ARG ALA ALA VAL ASP TYR GLN LYS VAL SEQRES 9 A 417 VAL ARG GLU ALA VAL LYS HIS ILE GLY TYR ASP ASP SER SEQRES 10 A 417 SER LYS GLY PHE ASP TYR LYS THR CYS ASN VAL LEU VAL SEQRES 11 A 417 ALA LEU GLU GLN GLN SER PRO ASP ILE ALA GLN GLY VAL SEQRES 12 A 417 HIS LEU ASP ARG ASN GLU GLU ASP ILE GLY ALA GLY ASP SEQRES 13 A 417 GLN GLY LEU MET PHE GLY TYR ALA THR ASP GLU THR GLU SEQRES 14 A 417 GLU CYS MET PRO LEU THR ILE VAL LEU ALA HIS LYS LEU SEQRES 15 A 417 ASN ALA LYS LEU ALA GLU LEU ARG ARG ASN GLY THR LEU SEQRES 16 A 417 PRO TRP LEU ARG PRO ASP SER LYS THR GLN VAL THR VAL SEQRES 17 A 417 GLN TYR MET GLN ASP ARG GLY ALA VAL LEU PRO ILE ARG SEQRES 18 A 417 VAL HIS THR ILE VAL ILE SER VAL GLN HIS ASP GLU GLU SEQRES 19 A 417 VAL CYS LEU ASP GLU MET ARG ASP ALA LEU LYS GLU LYS SEQRES 20 A 417 VAL ILE LYS ALA VAL VAL PRO ALA LYS TYR LEU ASP GLU SEQRES 21 A 417 ASP THR ILE TYR HIS LEU GLN PRO SER GLY ARG PHE VAL SEQRES 22 A 417 ILE GLY GLY PRO GLN GLY ASP ALA GLY LEU THR GLY ARG SEQRES 23 A 417 LYS ILE ILE VAL ASP THR TYR GLY GLY TRP GLY ALA HIS SEQRES 24 A 417 GLY GLY GLY ALA PHE SER GLY LYS ASP TYR THR LYS VAL SEQRES 25 A 417 ASP ARG SER ALA ALA TYR ALA ALA ARG TRP VAL ALA LYS SEQRES 26 A 417 SER LEU VAL LYS GLY GLY LEU CYS ARG ARG VAL LEU VAL SEQRES 27 A 417 GLN VAL SER TYR ALA ILE GLY VAL SER HIS PRO LEU SER SEQRES 28 A 417 ILE SER ILE PHE HIS TYR GLY THR SER GLN LYS SER GLU SEQRES 29 A 417 ARG GLU LEU LEU GLU ILE VAL LYS LYS ASN PHE ASP LEU SEQRES 30 A 417 ARG PRO GLY VAL ILE VAL ARG ASP LEU ASP LEU LYS LYS SEQRES 31 A 417 PRO ILE TYR GLN ARG THR ALA ALA TYR GLY HIS PHE GLY SEQRES 32 A 417 ARG ASP SER PHE PRO TRP GLU VAL PRO LYS LYS LEU LYS SEQRES 33 A 417 TYR HET MTA A 501 35 HET ALA A 502 9 HET MLA A 503 9 HET MGF A 504 4 HET GOL A 505 14 HET MG A 506 1 HET K A 507 1 HET NA A 508 1 HET NA A 509 1 HETNAM MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE HETNAM ALA ALANINE HETNAM MLA MALONIC ACID HETNAM MGF TRIFLUOROMAGNESATE HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION HETNAM NA SODIUM ION HETSYN MLA DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; HETSYN 2 MLA METHANEDICARBOXYLIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 MTA C11 H15 N5 O3 S FORMUL 3 ALA C3 H7 N O2 FORMUL 4 MLA C3 H4 O4 FORMUL 5 MGF F3 MG 1- FORMUL 6 GOL C3 H8 O3 FORMUL 7 MG MG 2+ FORMUL 8 K K 1+ FORMUL 9 NA 2(NA 1+) FORMUL 11 HOH *381(H2 O) HELIX 1 AA1 HIS A 29 ASP A 49 1 21 HELIX 2 AA2 TYR A 79 GLY A 91 1 13 HELIX 3 AA4 SER A 114 HIS A 122 1 9 HELIX 4 AA5 ASN A 126 ILE A 130 5 5 HELIX 5 AA6 LEU A 152 ASN A 170 1 19 HELIX 6 AA7 LEU A 215 LYS A 225 1 11 HELIX 7 AA8 VAL A 226 VAL A 230 1 5 HELIX 8 AB1 ASP A 291 GLY A 308 1 18 HELIX 9 AB3 SER A 341 PHE A 353 1 13 HELIX 10 AB4 ARG A 356 ASP A 365 1 10 HELIX 11 AB5 ILE A 370 ALA A 375 5 6 HELIX 12 AB6 PRO A 386 VAL A 389 4 4 SHEET 1 AA1 4 THR A 17 VAL A 25 0 SHEET 2 AA1 4 LEU A 176 ASP A 191 -1 O TYR A 188 N PHE A 18 SHEET 3 AA1 4 ALA A 194 HIS A 209 -1 O GLN A 208 N ASP A 179 SHEET 4 AA1 4 ILE A 241 LEU A 244 1 O HIS A 243 N ILE A 203 SHEET 1 AA2 3 ASN A 105 GLU A 111 0 SHEET 2 AA2 3 MET A 64 THR A 72 1 N LEU A 67 O ALA A 109 SHEET 3 AA2 3 LYS A 53 LYS A 61 -1 N LYS A 61 O MET A 64 SHEET 1 AA4 3 GLY A 136 THR A 143 0 SHEET 2 AA4 3 ARG A 313 TYR A 320 -1 O VAL A 316 N GLY A 140 SHEET 3 AA4 3 SER A 329 PHE A 333 -1 O PHE A 333 N LEU A 315 LINK OD2 ASP A 31 MG MG A 506 1555 1555 2.06 LINK OE2 GLU A 57 K K A 507 1555 2555 2.80 LINK O HIS A 201 NA NA A 509 1555 1555 2.84 LINK O ASP A 239 NA NA A 509 1555 1555 2.86 LINK OD1 ASP A 258 K K A 507 1555 1555 2.80 LINK O ALA A 259 K K A 507 1555 1555 2.86 LINK O VAL A 324 NA NA A 508 1555 1555 2.84 LINK O HIS A 326 NA NA A 508 1555 1555 2.86 LINK O1A MLA A 503 MG MG A 506 1555 1555 2.00 LINK O3B MLA A 503 MG MG A 506 1555 1555 2.03 LINK O3B MLA A 503 K K A 507 1555 1555 2.91 LINK MG MGF A 504 O HOH A 785 1555 1555 2.28 LINK MG MG A 506 O HOH A 631 1555 1555 2.14 LINK MG MG A 506 O HOH A 637 1555 1555 2.07 LINK K K A 507 O HOH A 631 1555 1555 3.25 LINK K K A 507 O HOH A 637 1555 1555 3.23 LINK K K A 507 O HOH A 686 1555 2555 2.85 CRYST1 67.981 94.122 117.315 90.00 90.00 90.00 I 2 2 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 0.014710 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010625 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008524 0.00000