HEADER TRANSFERASE/TRANSFERASE INHIBITOR 23-AUG-21 7RXW TITLE HUMAN METHIONINE ADENOSYLTRANSFERASE 2A BOUND TO METHYLTHIOADENOSINE TITLE 2 AND INHIBITOR IMIDO-DIPHOSPHATE (PNP) 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 7RXW 1 REMARK REVDAT 2 17-NOV-21 7RXW 1 JRNL REVDAT 1 10-NOV-21 7RXW 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) : 19.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 156783 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.128 REMARK 3 R VALUE (WORKING SET) : 0.128 REMARK 3 FREE R VALUE : 0.138 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 7777 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 19.8900 - 3.3200 1.00 5500 307 0.1305 0.1511 REMARK 3 2 3.3200 - 2.6400 1.00 5354 276 0.1318 0.1331 REMARK 3 3 2.6400 - 2.3000 1.00 5318 253 0.1270 0.1318 REMARK 3 4 2.3000 - 2.0900 1.00 5342 239 0.1220 0.1388 REMARK 3 5 2.0900 - 1.9400 1.00 5283 283 0.1204 0.1253 REMARK 3 6 1.9400 - 1.8300 1.00 5262 263 0.1270 0.1274 REMARK 3 7 1.8300 - 1.7400 1.00 5261 280 0.1230 0.1452 REMARK 3 8 1.7400 - 1.6600 1.00 5253 267 0.1220 0.1313 REMARK 3 9 1.6600 - 1.6000 1.00 5204 288 0.1219 0.1211 REMARK 3 10 1.6000 - 1.5400 1.00 5247 290 0.1174 0.1221 REMARK 3 11 1.5400 - 1.4900 1.00 5184 288 0.1204 0.1409 REMARK 3 12 1.4900 - 1.4500 1.00 5226 271 0.1218 0.1205 REMARK 3 13 1.4500 - 1.4100 1.00 5246 276 0.1258 0.1404 REMARK 3 14 1.4100 - 1.3800 1.00 5228 277 0.1265 0.1306 REMARK 3 15 1.3800 - 1.3500 1.00 5218 267 0.1288 0.1362 REMARK 3 16 1.3500 - 1.3200 1.00 5207 286 0.1291 0.1281 REMARK 3 17 1.3200 - 1.2900 1.00 5211 261 0.1265 0.1354 REMARK 3 18 1.2900 - 1.2700 1.00 5219 263 0.1272 0.1460 REMARK 3 19 1.2700 - 1.2500 1.00 5176 304 0.1306 0.1450 REMARK 3 20 1.2500 - 1.2200 1.00 5245 269 0.1264 0.1464 REMARK 3 21 1.2200 - 1.2100 1.00 5231 256 0.1287 0.1465 REMARK 3 22 1.2100 - 1.1900 1.00 5173 296 0.1318 0.1402 REMARK 3 23 1.1900 - 1.1700 0.98 5131 266 0.1378 0.1559 REMARK 3 24 1.1700 - 1.1500 0.96 4961 270 0.1383 0.1672 REMARK 3 25 1.1500 - 1.1400 0.92 4818 225 0.1389 0.1405 REMARK 3 26 1.1400 - 1.1200 0.87 4516 224 0.1420 0.1440 REMARK 3 27 1.1200 - 1.1100 0.79 4115 224 0.1442 0.1493 REMARK 3 28 1.1100 - 1.0900 0.72 3702 191 0.1463 0.1546 REMARK 3 29 1.0900 - 1.0800 0.64 3347 179 0.1591 0.1693 REMARK 3 30 1.0800 - 1.0700 0.55 2828 138 0.1649 0.1942 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) : 11.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.87 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): 6.2192 -12.1322 -47.8734 REMARK 3 T TENSOR REMARK 3 T11: 0.2028 T22: 0.2009 REMARK 3 T33: 0.1051 T12: -0.0176 REMARK 3 T13: 0.0180 T23: -0.0104 REMARK 3 L TENSOR REMARK 3 L11: 4.0287 L22: 5.0001 REMARK 3 L33: 5.3412 L12: -4.4808 REMARK 3 L13: -4.6316 L23: 5.1678 REMARK 3 S TENSOR REMARK 3 S11: 0.1667 S12: 1.0965 S13: -0.0114 REMARK 3 S21: -0.9955 S22: -0.0495 S23: -0.1958 REMARK 3 S31: -0.3961 S32: -0.0863 S33: -0.1137 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 19:80) REMARK 3 ORIGIN FOR THE GROUP (A): -10.1707 -4.7335 -13.5369 REMARK 3 T TENSOR REMARK 3 T11: 0.0733 T22: 0.0821 REMARK 3 T33: 0.0790 T12: 0.0061 REMARK 3 T13: 0.0027 T23: 0.0045 REMARK 3 L TENSOR REMARK 3 L11: 0.2214 L22: 0.2830 REMARK 3 L33: 0.4548 L12: -0.0701 REMARK 3 L13: -0.1364 L23: 0.0556 REMARK 3 S TENSOR REMARK 3 S11: -0.0329 S12: -0.0473 S13: -0.0076 REMARK 3 S21: 0.0519 S22: 0.0298 S23: 0.0362 REMARK 3 S31: 0.0204 S32: -0.0228 S33: 0.0021 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 81:89) REMARK 3 ORIGIN FOR THE GROUP (A): -11.8987 -14.1310 -7.1659 REMARK 3 T TENSOR REMARK 3 T11: 0.0683 T22: 0.1160 REMARK 3 T33: 0.0786 T12: -0.0126 REMARK 3 T13: 0.0104 T23: 0.0099 REMARK 3 L TENSOR REMARK 3 L11: 3.4186 L22: 9.0968 REMARK 3 L33: 4.9563 L12: -2.7069 REMARK 3 L13: -1.3731 L23: 2.6664 REMARK 3 S TENSOR REMARK 3 S11: -0.0750 S12: 0.0729 S13: -0.2172 REMARK 3 S21: -0.0272 S22: -0.0284 S23: 0.4717 REMARK 3 S31: 0.1083 S32: -0.5022 S33: 0.1082 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 90:176) REMARK 3 ORIGIN FOR THE GROUP (A): -9.4611 -7.5607 -20.2214 REMARK 3 T TENSOR REMARK 3 T11: 0.0505 T22: 0.0831 REMARK 3 T33: 0.0863 T12: -0.0133 REMARK 3 T13: 0.0003 T23: -0.0014 REMARK 3 L TENSOR REMARK 3 L11: 0.0871 L22: 0.5357 REMARK 3 L33: 0.3294 L12: -0.1031 REMARK 3 L13: -0.0056 L23: -0.0245 REMARK 3 S TENSOR REMARK 3 S11: -0.0080 S12: -0.0151 S13: -0.0116 REMARK 3 S21: 0.0167 S22: 0.0049 S23: 0.0401 REMARK 3 S31: 0.0070 S32: -0.0309 S33: 0.0046 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 177:192) REMARK 3 ORIGIN FOR THE GROUP (A): 2.0322 -16.1670 -34.9173 REMARK 3 T TENSOR REMARK 3 T11: 0.0637 T22: 0.0365 REMARK 3 T33: 0.0680 T12: 0.0060 REMARK 3 T13: 0.0015 T23: -0.0148 REMARK 3 L TENSOR REMARK 3 L11: 1.3186 L22: 1.2240 REMARK 3 L33: 2.0771 L12: 0.1077 REMARK 3 L13: -0.4176 L23: -0.1915 REMARK 3 S TENSOR REMARK 3 S11: -0.0335 S12: 0.1086 S13: -0.0122 REMARK 3 S21: -0.1438 S22: -0.0258 S23: -0.0089 REMARK 3 S31: -0.0093 S32: 0.0644 S33: 0.0149 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 193:296) REMARK 3 ORIGIN FOR THE GROUP (A): 1.2929 -16.2409 -27.0329 REMARK 3 T TENSOR REMARK 3 T11: 0.0683 T22: 0.0725 REMARK 3 T33: 0.0766 T12: -0.0055 REMARK 3 T13: 0.0005 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 0.4322 L22: 0.5637 REMARK 3 L33: 0.2393 L12: -0.2260 REMARK 3 L13: 0.0407 L23: -0.0042 REMARK 3 S TENSOR REMARK 3 S11: -0.0104 S12: 0.0051 S13: -0.0544 REMARK 3 S21: -0.0113 S22: 0.0221 S23: -0.0050 REMARK 3 S31: 0.0321 S32: 0.0181 S33: -0.0123 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 297:402) REMARK 3 ORIGIN FOR THE GROUP (A): -16.2462 -0.8126 -36.3825 REMARK 3 T TENSOR REMARK 3 T11: 0.0681 T22: 0.0646 REMARK 3 T33: 0.0672 T12: -0.0084 REMARK 3 T13: -0.0136 T23: -0.0034 REMARK 3 L TENSOR REMARK 3 L11: 0.4289 L22: 0.5425 REMARK 3 L33: 0.3633 L12: -0.1698 REMARK 3 L13: -0.0419 L23: -0.0078 REMARK 3 S TENSOR REMARK 3 S11: 0.0021 S12: 0.0441 S13: -0.0227 REMARK 3 S21: -0.0872 S22: 0.0033 S23: 0.0816 REMARK 3 S31: 0.0204 S32: -0.0588 S33: -0.0072 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 7RXW 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_1000259194. 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 : 7.0 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 : 160734 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.050 REMARK 200 RESOLUTION RANGE LOW (A) : 19.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 40.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.38800 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 (%): 39.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM AMMONIUM CITRATE AND 12% PEG REMARK 280 -3350, PH 7.0, 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 34.16100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.03450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 58.67200 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 34.16100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.03450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 58.67200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 34.16100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.03450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 58.67200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 34.16100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.03450 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 58.67200 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: 9630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 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 634 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 798 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 816 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 910 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 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 1.35 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 CYS A 149 30.96 70.05 REMARK 500 VAL A 226 -66.02 -109.41 REMARK 500 THR A 270 -102.93 -122.18 REMARK 500 ARG A 292 -60.39 -92.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 264 0.08 SIDE CHAIN 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 911 DISTANCE = 6.11 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 405 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 31 OD2 REMARK 620 2 2PN A 403 O3 81.9 REMARK 620 3 2PN A 403 O6 176.6 97.0 REMARK 620 4 HOH A 520 O 91.2 171.6 90.2 REMARK 620 5 HOH A 526 O 90.0 90.9 93.2 84.3 REMARK 620 6 HOH A 557 O 90.9 91.0 85.9 93.9 178.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 407 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 57 OE2 REMARK 620 2 ASP A 258 OD1 42.0 REMARK 620 3 ALA A 259 O 38.3 6.3 REMARK 620 4 2PN A 403 O6 42.7 10.4 15.7 REMARK 620 5 HOH A 520 O 39.4 7.3 11.5 4.7 REMARK 620 6 HOH A 526 O 34.5 8.5 9.3 9.9 5.5 REMARK 620 7 HOH A 544 O 51.5 10.2 13.3 17.5 16.4 18.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 406 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 291 OD2 REMARK 620 2 2PN A 403 O1 93.7 REMARK 620 3 2PN A 403 O4 102.7 9.1 REMARK 620 4 HOH A 506 O 104.5 10.9 3.1 REMARK 620 5 HOH A 518 O 100.1 7.2 5.3 4.9 REMARK 620 6 HOH A 552 O 96.8 4.1 7.1 7.9 3.4 REMARK 620 7 HOH A 684 O 95.2 8.8 12.5 11.9 7.2 6.2 REMARK 620 N 1 2 3 4 5 6 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: 7RXV RELATED DB: PDB REMARK 900 RELATED ID: 7RXX RELATED DB: PDB DBREF 7RXW A 1 395 UNP P31153 METK2_HUMAN 1 395 SEQADV 7RXW MET A -21 UNP P31153 EXPRESSION TAG SEQADV 7RXW HIS A -20 UNP P31153 EXPRESSION TAG SEQADV 7RXW HIS A -19 UNP P31153 EXPRESSION TAG SEQADV 7RXW HIS A -18 UNP P31153 EXPRESSION TAG SEQADV 7RXW HIS A -17 UNP P31153 EXPRESSION TAG SEQADV 7RXW HIS A -16 UNP P31153 EXPRESSION TAG SEQADV 7RXW HIS A -15 UNP P31153 EXPRESSION TAG SEQADV 7RXW SER A -14 UNP P31153 EXPRESSION TAG SEQADV 7RXW SER A -13 UNP P31153 EXPRESSION TAG SEQADV 7RXW GLY A -12 UNP P31153 EXPRESSION TAG SEQADV 7RXW VAL A -11 UNP P31153 EXPRESSION TAG SEQADV 7RXW ASP A -10 UNP P31153 EXPRESSION TAG SEQADV 7RXW LEU A -9 UNP P31153 EXPRESSION TAG SEQADV 7RXW GLY A -8 UNP P31153 EXPRESSION TAG SEQADV 7RXW THR A -7 UNP P31153 EXPRESSION TAG SEQADV 7RXW GLU A -6 UNP P31153 EXPRESSION TAG SEQADV 7RXW ASN A -5 UNP P31153 EXPRESSION TAG SEQADV 7RXW LEU A -4 UNP P31153 EXPRESSION TAG SEQADV 7RXW TYR A -3 UNP P31153 EXPRESSION TAG SEQADV 7RXW PHE A -2 UNP P31153 EXPRESSION TAG SEQADV 7RXW GLN A -1 UNP P31153 EXPRESSION TAG SEQADV 7RXW 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 401 35 HET ALA A 402 10 HET 2PN A 403 10 HET EDO A 404 10 HET MG A 405 1 HET MG A 406 1 HET K A 407 1 HETNAM MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE HETNAM ALA ALANINE HETNAM 2PN IMIDODIPHOSPHORIC ACID HETNAM EDO 1,2-ETHANEDIOL HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 MTA C11 H15 N5 O3 S FORMUL 3 ALA C3 H7 N O2 FORMUL 4 2PN H5 N O6 P2 FORMUL 5 EDO C2 H6 O2 FORMUL 6 MG 2(MG 2+) FORMUL 8 K K 1+ FORMUL 9 HOH *411(H2 O) HELIX 1 AA1 HIS A 29 ASP A 49 1 21 HELIX 2 AA2 ASP A 78 GLY A 91 1 14 HELIX 3 AA3 SER A 95 GLY A 98 5 4 HELIX 4 AA4 SER A 114 HIS A 122 1 9 HELIX 5 AA5 ASN A 126 ILE A 130 5 5 HELIX 6 AA6 PRO A 151 ASN A 170 1 20 HELIX 7 AA7 CYS A 214 LYS A 225 1 12 HELIX 8 AA8 VAL A 226 VAL A 231 1 6 HELIX 9 AA9 PRO A 232 LEU A 236 5 5 HELIX 10 AB1 GLY A 253 GLY A 257 5 5 HELIX 11 AB2 LYS A 289 GLY A 308 1 20 HELIX 12 AB3 SER A 341 PHE A 353 1 13 HELIX 13 AB4 ARG A 356 ASP A 365 1 10 HELIX 14 AB5 ILE A 370 ALA A 375 5 6 HELIX 15 AB6 PHE A 385 VAL A 389 5 5 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 4 ASN A 105 GLU A 111 0 SHEET 2 AA2 4 MET A 64 THR A 72 1 N LEU A 67 O ALA A 109 SHEET 3 AA2 4 LYS A 53 LYS A 61 -1 N LYS A 61 O MET A 64 SHEET 4 AA2 4 GLY A 260 LEU A 261 -1 O GLY A 260 N ALA A 60 SHEET 1 AA3 2 ASP A 93 ASP A 94 0 SHEET 2 AA3 2 PHE A 99 ASP A 100 -1 O PHE A 99 N ASP A 94 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 405 1555 1555 2.08 LINK OE2 GLU A 57 K K A 407 1555 2555 2.80 LINK OD1 ASP A 258 K K A 407 1555 1555 2.80 LINK O ALA A 259 K K A 407 1555 1555 2.86 LINK OD2 ASP A 291 MG MG A 406 1555 2555 2.20 LINK O3 2PN A 403 MG MG A 405 1555 1555 2.01 LINK O6 2PN A 403 MG MG A 405 1555 1555 2.02 LINK O1 2PN A 403 MG MG A 406 1555 1555 2.17 LINK O4 2PN A 403 MG MG A 406 1555 1555 2.04 LINK O6 2PN A 403 K K A 407 1555 1555 2.99 LINK MG MG A 405 O HOH A 520 1555 1555 2.14 LINK MG MG A 405 O HOH A 526 1555 1555 2.12 LINK MG MG A 405 O HOH A 557 1555 1555 1.90 LINK MG MG A 406 O HOH A 506 1555 1555 3.00 LINK MG MG A 406 O HOH A 518 1555 2555 2.04 LINK MG MG A 406 O HOH A 552 1555 1555 2.01 LINK MG MG A 406 O HOH A 684 1555 2555 2.03 LINK K K A 407 O HOH A 520 1555 1555 3.39 LINK K K A 407 O HOH A 526 1555 1555 3.36 LINK K K A 407 O HOH A 544 1555 2555 2.87 CRYST1 68.322 94.069 117.344 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 0.014637 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010630 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008522 0.00000