HEADER TRANSFERASE 21-APR-14 4PDS TITLE CRYSTAL STRUCTURE OF RAD53 KINASE DOMAIN AND SCD2 IN COMPLEX WITH TITLE 2 AMPPNP COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE RAD53; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: KINASE DOMAIN AND SCD2 (UNP RESIDUES 170-512); COMPND 5 SYNONYM: CHEK2 HOMOLOG,SERINE-PROTEIN KINASE 1; COMPND 6 EC: 2.7.12.1; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: RAD53, MEC2, SAD1, SPK1, YPL153C, P2588; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPROEX-HTA-TEV KEYWDS KINASE DOMAIN, ANP, C-LOBE, ACTIVATION SEGMENT EXCHANGE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.S.HO,L.E.WYBENGA-GROOT,D.F.CECCARELLI,F.SICHERI REVDAT 6 27-SEP-23 4PDS 1 REMARK REVDAT 5 08-JAN-20 4PDS 1 REMARK REVDAT 4 17-JUL-19 4PDS 1 REMARK REVDAT 3 22-NOV-17 4PDS 1 SOURCE REMARK REVDAT 2 01-OCT-14 4PDS 1 JRNL REVDAT 1 28-MAY-14 4PDS 0 JRNL AUTH L.E.WYBENGA-GROOT,C.S.HO,F.D.SWEENEY,D.F.CECCARELLI, JRNL AUTH 2 C.J.MCGLADE,D.DUROCHER,F.SICHERI JRNL TITL STRUCTURAL BASIS OF RAD53 KINASE ACTIVATION BY DIMERIZATION JRNL TITL 2 AND ACTIVATION SEGMENT EXCHANGE. JRNL REF CELL SIGNAL. V. 26 1825 2014 JRNL REFN ESSN 1873-3913 JRNL PMID 24815189 JRNL DOI 10.1016/J.CELLSIG.2014.05.004 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 14317 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 726 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 29.2144 - 4.9531 0.95 2733 140 0.2480 0.2728 REMARK 3 2 4.9531 - 3.9344 1.00 2791 129 0.2044 0.2358 REMARK 3 3 3.9344 - 3.4380 1.00 2746 156 0.2051 0.2598 REMARK 3 4 3.4380 - 3.1240 1.00 2708 144 0.2268 0.2541 REMARK 3 5 3.1240 - 2.9000 0.96 2613 157 0.2624 0.3196 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 83.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 90.69 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 : 0.005 3681 REMARK 3 ANGLE : 0.894 5013 REMARK 3 CHIRALITY : 0.036 609 REMARK 3 PLANARITY : 0.008 621 REMARK 3 DIHEDRAL : 13.333 1213 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -12.9148 -4.7564 -27.8893 REMARK 3 T TENSOR REMARK 3 T11: 0.5740 T22: 0.5785 REMARK 3 T33: 0.4596 T12: 0.1992 REMARK 3 T13: -0.1263 T23: -0.1844 REMARK 3 L TENSOR REMARK 3 L11: 1.9948 L22: 2.1492 REMARK 3 L33: 0.8566 L12: -1.5288 REMARK 3 L13: 0.6180 L23: -0.3443 REMARK 3 S TENSOR REMARK 3 S11: -0.0523 S12: 0.0344 S13: -0.0188 REMARK 3 S21: -0.0575 S22: 0.0210 S23: 0.0853 REMARK 3 S31: -0.1198 S32: -0.0516 S33: 0.0415 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 4PDS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000201196. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XDS, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14414 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 8.500 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.64800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 4PDP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% V/V PEG400, 50 MM SODIUM CITRATE, REMARK 280 100 MM TRIS, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z 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 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 111.08500 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 111.08500 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 37.07450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.76950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 37.07450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.76950 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 111.08500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 37.07450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 38.76950 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 111.08500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 37.07450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 38.76950 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 -74.14900 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -111.08500 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 APPLY THE FOLLOWING TO CHAINS: B 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 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 GLY A 166 REMARK 465 ALA A 167 REMARK 465 MET A 168 REMARK 465 ALA A 169 REMARK 465 THR A 170 REMARK 465 SER A 171 REMARK 465 LYS A 172 REMARK 465 ILE A 173 REMARK 465 ALA A 174 REMARK 465 SER A 175 REMARK 465 PRO A 176 REMARK 465 GLY A 177 REMARK 465 LEU A 178 REMARK 465 THR A 179 REMARK 465 SER A 180 REMARK 465 SER A 181 REMARK 465 THR A 182 REMARK 465 ALA A 183 REMARK 465 SER A 184 REMARK 465 SER A 185 REMARK 465 MET A 186 REMARK 465 VAL A 187 REMARK 465 ALA A 188 REMARK 465 ASN A 189 REMARK 465 LYS A 190 REMARK 465 VAL A 204 REMARK 465 GLY A 205 REMARK 465 GLN A 206 REMARK 465 GLY A 207 REMARK 465 ALA A 208 REMARK 465 PHE A 209 REMARK 465 ALA A 210 REMARK 465 SER A 230 REMARK 465 LYS A 231 REMARK 465 ARG A 232 REMARK 465 LYS A 233 REMARK 465 VAL A 234 REMARK 465 ILE A 235 REMARK 465 GLY A 236 REMARK 465 ASN A 237 REMARK 465 MET A 238 REMARK 465 ASP A 239 REMARK 465 GLY A 240 REMARK 465 GLU A 264 REMARK 465 ASP A 265 REMARK 465 THR A 266 REMARK 465 GLN A 346 REMARK 465 GLY A 347 REMARK 465 ASN A 348 REMARK 465 GLY A 349 REMARK 465 SER A 350 REMARK 465 PHE A 351 REMARK 465 MET A 352 REMARK 465 LYS A 353 REMARK 465 THR A 354 REMARK 465 PHE A 355 REMARK 465 CYS A 356 REMARK 465 GLY A 357 REMARK 465 THR A 358 REMARK 465 LEU A 359 REMARK 465 GLY A 369 REMARK 465 LYS A 370 REMARK 465 ASP A 371 REMARK 465 THR A 372 REMARK 465 SER A 373 REMARK 465 VAL A 374 REMARK 465 SER A 375 REMARK 465 PRO A 376 REMARK 465 ASP A 377 REMARK 465 GLU A 378 REMARK 465 TYR A 379 REMARK 465 GLU A 380 REMARK 465 GLU A 381 REMARK 465 GLY A 472 REMARK 465 SER A 473 REMARK 465 GLN A 474 REMARK 465 GLN A 491 REMARK 465 LYS A 492 REMARK 465 LEU A 493 REMARK 465 LEU A 494 REMARK 465 GLU A 495 REMARK 465 ASN A 496 REMARK 465 MET A 497 REMARK 465 ASP A 498 REMARK 465 ASP A 499 REMARK 465 ALA A 500 REMARK 465 GLN A 501 REMARK 465 TYR A 502 REMARK 465 GLU A 503 REMARK 465 PHE A 504 REMARK 465 VAL A 505 REMARK 465 LYS A 506 REMARK 465 ALA A 507 REMARK 465 GLN A 508 REMARK 465 ARG A 509 REMARK 465 LYS A 510 REMARK 465 LEU A 511 REMARK 465 GLN A 512 REMARK 465 GLY B 166 REMARK 465 ALA B 167 REMARK 465 MET B 168 REMARK 465 ALA B 169 REMARK 465 THR B 170 REMARK 465 SER B 171 REMARK 465 LYS B 172 REMARK 465 ILE B 173 REMARK 465 ALA B 174 REMARK 465 SER B 175 REMARK 465 PRO B 176 REMARK 465 GLY B 177 REMARK 465 LEU B 178 REMARK 465 THR B 179 REMARK 465 SER B 180 REMARK 465 SER B 181 REMARK 465 THR B 182 REMARK 465 ALA B 183 REMARK 465 SER B 184 REMARK 465 SER B 185 REMARK 465 MET B 186 REMARK 465 VAL B 187 REMARK 465 ALA B 188 REMARK 465 ASN B 189 REMARK 465 LYS B 190 REMARK 465 ASP B 201 REMARK 465 GLU B 202 REMARK 465 VAL B 203 REMARK 465 VAL B 204 REMARK 465 GLY B 205 REMARK 465 GLN B 206 REMARK 465 GLY B 207 REMARK 465 ALA B 208 REMARK 465 PHE B 209 REMARK 465 SER B 230 REMARK 465 LYS B 231 REMARK 465 ARG B 232 REMARK 465 LYS B 233 REMARK 465 VAL B 234 REMARK 465 ILE B 235 REMARK 465 GLY B 236 REMARK 465 ASN B 237 REMARK 465 MET B 238 REMARK 465 ASP B 239 REMARK 465 GLY B 240 REMARK 465 GLU B 264 REMARK 465 ASP B 265 REMARK 465 THR B 266 REMARK 465 GLU B 267 REMARK 465 SER B 268 REMARK 465 GLN B 346 REMARK 465 GLY B 347 REMARK 465 ASN B 348 REMARK 465 GLY B 349 REMARK 465 SER B 350 REMARK 465 PHE B 351 REMARK 465 MET B 352 REMARK 465 LYS B 353 REMARK 465 THR B 354 REMARK 465 PHE B 355 REMARK 465 CYS B 356 REMARK 465 GLY B 357 REMARK 465 ARG B 368 REMARK 465 GLY B 369 REMARK 465 LYS B 370 REMARK 465 ASP B 371 REMARK 465 THR B 372 REMARK 465 SER B 373 REMARK 465 VAL B 374 REMARK 465 SER B 375 REMARK 465 PRO B 376 REMARK 465 ASP B 377 REMARK 465 GLU B 378 REMARK 465 TYR B 379 REMARK 465 GLU B 380 REMARK 465 GLU B 381 REMARK 465 ARG B 382 REMARK 465 GLY B 472 REMARK 465 SER B 473 REMARK 465 GLN B 474 REMARK 465 SER B 475 REMARK 465 GLU B 495 REMARK 465 ASN B 496 REMARK 465 MET B 497 REMARK 465 ASP B 498 REMARK 465 ASP B 499 REMARK 465 ALA B 500 REMARK 465 GLN B 501 REMARK 465 TYR B 502 REMARK 465 GLU B 503 REMARK 465 PHE B 504 REMARK 465 VAL B 505 REMARK 465 LYS B 506 REMARK 465 ALA B 507 REMARK 465 GLN B 508 REMARK 465 ARG B 509 REMARK 465 LYS B 510 REMARK 465 LEU B 511 REMARK 465 GLN B 512 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 THR A 191 OG1 CG2 REMARK 470 ASP A 201 CG OD1 OD2 REMARK 470 GLU A 202 CG CD OE1 OE2 REMARK 470 VAL A 203 CG1 CG2 REMARK 470 LYS A 213 CG CD CE NZ REMARK 470 LYS A 227 CG CD CE NZ REMARK 470 ARG A 243 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 244 CG CD OE1 OE2 REMARK 470 LEU A 245 CG CD1 CD2 REMARK 470 GLU A 246 CG CD OE1 OE2 REMARK 470 GLN A 249 CG CD OE1 NE2 REMARK 470 LYS A 250 CG CD CE NZ REMARK 470 TYR A 269 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 298 CG CD OE1 OE2 REMARK 470 ARG A 318 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 319 CG OD1 OD2 REMARK 470 LYS A 321 CG CD CE NZ REMARK 470 ASP A 323 CG OD1 OD2 REMARK 470 GLU A 328 CG CD OE1 OE2 REMARK 470 ASP A 330 CG OD1 OD2 REMARK 470 ASP A 331 CG OD1 OD2 REMARK 470 LYS A 344 CG CD CE NZ REMARK 470 VAL A 345 CG1 CG2 REMARK 470 VAL A 366 CG1 CG2 REMARK 470 ILE A 367 CG1 CG2 CD1 REMARK 470 ARG A 368 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 382 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 383 CG OD1 ND2 REMARK 470 GLU A 384 CG CD OE1 OE2 REMARK 470 THR A 412 OG1 CG2 REMARK 470 GLN A 413 CG CD OE1 NE2 REMARK 470 ASP A 414 CG OD1 OD2 REMARK 470 GLN A 415 CG CD OE1 NE2 REMARK 470 LEU A 416 CG CD1 CD2 REMARK 470 TYR A 417 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 418 CG CD CE NZ REMARK 470 GLN A 419 CG CD OE1 NE2 REMARK 470 ARG A 422 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 427 CG CD OE1 OE2 REMARK 470 LYS A 431 CG CD CE NZ REMARK 470 ASP A 432 CG OD1 OD2 REMARK 470 ARG A 434 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 437 CG CD OE1 OE2 REMARK 470 GLU A 438 CG CD OE1 OE2 REMARK 470 ARG A 440 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 459 CG CD CE NZ REMARK 470 LEU A 471 CG CD1 CD2 REMARK 470 TYR A 476 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN A 486 CG CD OE1 NE2 REMARK 470 LEU A 488 CG CD1 CD2 REMARK 470 GLN A 490 CG CD OE1 NE2 REMARK 470 THR B 191 OG1 CG2 REMARK 470 LYS B 195 CG CD CE NZ REMARK 470 LYS B 222 CG CD CE NZ REMARK 470 LYS B 227 CG CD CE NZ REMARK 470 ILE B 229 CG1 CG2 CD1 REMARK 470 ARG B 243 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 244 CG CD OE1 OE2 REMARK 470 GLU B 246 CG CD OE1 OE2 REMARK 470 LYS B 250 CG CD CE NZ REMARK 470 ASN B 252 CG OD1 ND2 REMARK 470 LYS B 260 CG CD CE NZ REMARK 470 ARG B 318 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 321 CG CD CE NZ REMARK 470 ASP B 323 CG OD1 OD2 REMARK 470 GLU B 328 CG CD OE1 OE2 REMARK 470 LYS B 344 CG CD CE NZ REMARK 470 LEU B 359 CG CD1 CD2 REMARK 470 GLU B 384 CG CD OE1 OE2 REMARK 470 TYR B 385 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN B 413 CG CD OE1 NE2 REMARK 470 ASP B 414 CG OD1 OD2 REMARK 470 GLN B 415 CG CD OE1 NE2 REMARK 470 TYR B 417 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS B 418 CG CD CE NZ REMARK 470 GLN B 419 CG CD OE1 NE2 REMARK 470 ARG B 422 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 427 CG CD OE1 OE2 REMARK 470 LYS B 431 CG CD CE NZ REMARK 470 ASP B 432 CG OD1 OD2 REMARK 470 ARG B 434 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 437 CG CD OE1 OE2 REMARK 470 ARG B 440 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 444 CG OD1 OD2 REMARK 470 ASP B 450 CG OD1 OD2 REMARK 470 LYS B 459 CG CD CE NZ REMARK 470 ILE B 482 CG1 CG2 CD1 REMARK 470 GLN B 486 CG CD OE1 NE2 REMARK 470 LYS B 492 CG CD CE NZ REMARK 470 LEU B 493 CG CD1 CD2 REMARK 470 LEU B 494 CG CD1 CD2 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 GLU A 202 -136.63 -86.81 REMARK 500 ASP A 319 45.16 -156.67 REMARK 500 ASP A 330 -60.46 -105.80 REMARK 500 PRO A 332 71.04 19.59 REMARK 500 ALA A 339 71.79 59.64 REMARK 500 GLU A 365 -9.84 -58.09 REMARK 500 ILE A 367 -79.88 -81.55 REMARK 500 ASN A 383 65.72 -172.81 REMARK 500 SER A 409 -155.19 -133.31 REMARK 500 SER A 411 -79.72 -96.63 REMARK 500 GLN A 413 2.74 -45.35 REMARK 500 LEU A 416 -72.35 -69.34 REMARK 500 ASP B 319 44.69 -156.09 REMARK 500 PRO B 332 74.81 18.55 REMARK 500 ALA B 339 70.83 58.98 REMARK 500 SER B 409 -158.81 -132.96 REMARK 500 SER B 411 -85.92 -92.60 REMARK 500 GLN B 413 20.60 -65.82 REMARK 500 LEU B 416 -72.00 -76.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 ANP A 601 REMARK 610 ANP B 601 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ANP A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ANP B 601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4PDP RELATED DB: PDB REMARK 900 RAD53 KINASE DOMAIN AND SCD2 IN APO FORM AT HIGHER RESOLUTION DBREF 4PDS A 170 512 UNP P22216 RAD53_YEAST 170 512 DBREF 4PDS B 170 512 UNP P22216 RAD53_YEAST 170 512 SEQADV 4PDS GLY A 166 UNP P22216 EXPRESSION TAG SEQADV 4PDS ALA A 167 UNP P22216 EXPRESSION TAG SEQADV 4PDS MET A 168 UNP P22216 EXPRESSION TAG SEQADV 4PDS ALA A 169 UNP P22216 EXPRESSION TAG SEQADV 4PDS SER A 225 UNP P22216 ALA 225 ENGINEERED MUTATION SEQADV 4PDS ALA A 339 UNP P22216 ASP 339 ENGINEERED MUTATION SEQADV 4PDS GLY B 166 UNP P22216 EXPRESSION TAG SEQADV 4PDS ALA B 167 UNP P22216 EXPRESSION TAG SEQADV 4PDS MET B 168 UNP P22216 EXPRESSION TAG SEQADV 4PDS ALA B 169 UNP P22216 EXPRESSION TAG SEQADV 4PDS SER B 225 UNP P22216 ALA 225 ENGINEERED MUTATION SEQADV 4PDS ALA B 339 UNP P22216 ASP 339 ENGINEERED MUTATION SEQRES 1 A 347 GLY ALA MET ALA THR SER LYS ILE ALA SER PRO GLY LEU SEQRES 2 A 347 THR SER SER THR ALA SER SER MET VAL ALA ASN LYS THR SEQRES 3 A 347 GLY ILE PHE LYS ASP PHE SER ILE ILE ASP GLU VAL VAL SEQRES 4 A 347 GLY GLN GLY ALA PHE ALA THR VAL LYS LYS ALA ILE GLU SEQRES 5 A 347 ARG THR THR GLY LYS THR PHE SER VAL LYS ILE ILE SER SEQRES 6 A 347 LYS ARG LYS VAL ILE GLY ASN MET ASP GLY VAL THR ARG SEQRES 7 A 347 GLU LEU GLU VAL LEU GLN LYS LEU ASN HIS PRO ARG ILE SEQRES 8 A 347 VAL ARG LEU LYS GLY PHE TYR GLU ASP THR GLU SER TYR SEQRES 9 A 347 TYR MET VAL MET GLU PHE VAL SER GLY GLY ASP LEU MET SEQRES 10 A 347 ASP PHE VAL ALA ALA HIS GLY ALA VAL GLY GLU ASP ALA SEQRES 11 A 347 GLY ARG GLU ILE SER ARG GLN ILE LEU THR ALA ILE LYS SEQRES 12 A 347 TYR ILE HIS SER MET GLY ILE SER HIS ARG ASP LEU LYS SEQRES 13 A 347 PRO ASP ASN ILE LEU ILE GLU GLN ASP ASP PRO VAL LEU SEQRES 14 A 347 VAL LYS ILE THR ALA PHE GLY LEU ALA LYS VAL GLN GLY SEQRES 15 A 347 ASN GLY SER PHE MET LYS THR PHE CYS GLY THR LEU ALA SEQRES 16 A 347 TYR VAL ALA PRO GLU VAL ILE ARG GLY LYS ASP THR SER SEQRES 17 A 347 VAL SER PRO ASP GLU TYR GLU GLU ARG ASN GLU TYR SER SEQRES 18 A 347 SER LEU VAL ASP MET TRP SER MET GLY CYS LEU VAL TYR SEQRES 19 A 347 VAL ILE LEU THR GLY HIS LEU PRO PHE SER GLY SER THR SEQRES 20 A 347 GLN ASP GLN LEU TYR LYS GLN ILE GLY ARG GLY SER TYR SEQRES 21 A 347 HIS GLU GLY PRO LEU LYS ASP PHE ARG ILE SER GLU GLU SEQRES 22 A 347 ALA ARG ASP PHE ILE ASP SER LEU LEU GLN VAL ASP PRO SEQRES 23 A 347 ASN ASN ARG SER THR ALA ALA LYS ALA LEU ASN HIS PRO SEQRES 24 A 347 TRP ILE LYS MET SER PRO LEU GLY SER GLN SER TYR GLY SEQRES 25 A 347 ASP PHE SER GLN ILE SER LEU SER GLN SER LEU SER GLN SEQRES 26 A 347 GLN LYS LEU LEU GLU ASN MET ASP ASP ALA GLN TYR GLU SEQRES 27 A 347 PHE VAL LYS ALA GLN ARG LYS LEU GLN SEQRES 1 B 347 GLY ALA MET ALA THR SER LYS ILE ALA SER PRO GLY LEU SEQRES 2 B 347 THR SER SER THR ALA SER SER MET VAL ALA ASN LYS THR SEQRES 3 B 347 GLY ILE PHE LYS ASP PHE SER ILE ILE ASP GLU VAL VAL SEQRES 4 B 347 GLY GLN GLY ALA PHE ALA THR VAL LYS LYS ALA ILE GLU SEQRES 5 B 347 ARG THR THR GLY LYS THR PHE SER VAL LYS ILE ILE SER SEQRES 6 B 347 LYS ARG LYS VAL ILE GLY ASN MET ASP GLY VAL THR ARG SEQRES 7 B 347 GLU LEU GLU VAL LEU GLN LYS LEU ASN HIS PRO ARG ILE SEQRES 8 B 347 VAL ARG LEU LYS GLY PHE TYR GLU ASP THR GLU SER TYR SEQRES 9 B 347 TYR MET VAL MET GLU PHE VAL SER GLY GLY ASP LEU MET SEQRES 10 B 347 ASP PHE VAL ALA ALA HIS GLY ALA VAL GLY GLU ASP ALA SEQRES 11 B 347 GLY ARG GLU ILE SER ARG GLN ILE LEU THR ALA ILE LYS SEQRES 12 B 347 TYR ILE HIS SER MET GLY ILE SER HIS ARG ASP LEU LYS SEQRES 13 B 347 PRO ASP ASN ILE LEU ILE GLU GLN ASP ASP PRO VAL LEU SEQRES 14 B 347 VAL LYS ILE THR ALA PHE GLY LEU ALA LYS VAL GLN GLY SEQRES 15 B 347 ASN GLY SER PHE MET LYS THR PHE CYS GLY THR LEU ALA SEQRES 16 B 347 TYR VAL ALA PRO GLU VAL ILE ARG GLY LYS ASP THR SER SEQRES 17 B 347 VAL SER PRO ASP GLU TYR GLU GLU ARG ASN GLU TYR SER SEQRES 18 B 347 SER LEU VAL ASP MET TRP SER MET GLY CYS LEU VAL TYR SEQRES 19 B 347 VAL ILE LEU THR GLY HIS LEU PRO PHE SER GLY SER THR SEQRES 20 B 347 GLN ASP GLN LEU TYR LYS GLN ILE GLY ARG GLY SER TYR SEQRES 21 B 347 HIS GLU GLY PRO LEU LYS ASP PHE ARG ILE SER GLU GLU SEQRES 22 B 347 ALA ARG ASP PHE ILE ASP SER LEU LEU GLN VAL ASP PRO SEQRES 23 B 347 ASN ASN ARG SER THR ALA ALA LYS ALA LEU ASN HIS PRO SEQRES 24 B 347 TRP ILE LYS MET SER PRO LEU GLY SER GLN SER TYR GLY SEQRES 25 B 347 ASP PHE SER GLN ILE SER LEU SER GLN SER LEU SER GLN SEQRES 26 B 347 GLN LYS LEU LEU GLU ASN MET ASP ASP ALA GLN TYR GLU SEQRES 27 B 347 PHE VAL LYS ALA GLN ARG LYS LEU GLN HET ANP A 601 27 HET ANP B 601 23 HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER FORMUL 3 ANP 2(C10 H17 N6 O12 P3) HELIX 1 AA1 GLY A 192 ASP A 196 1 5 HELIX 2 AA2 ARG A 243 LEU A 251 1 9 HELIX 3 AA3 ASP A 280 GLY A 289 1 10 HELIX 4 AA4 GLY A 292 MET A 313 1 22 HELIX 5 AA5 ALA A 363 ILE A 367 5 5 HELIX 6 AA6 TYR A 385 GLY A 404 1 20 HELIX 7 AA7 ASP A 414 ARG A 422 1 9 HELIX 8 AA8 HIS A 426 PHE A 433 1 8 HELIX 9 AA9 SER A 436 LEU A 447 1 12 HELIX 10 AB1 ASP A 450 ARG A 454 5 5 HELIX 11 AB2 THR A 456 ASN A 462 1 7 HELIX 12 AB3 HIS A 463 MET A 468 1 6 HELIX 13 AB4 SER A 483 GLN A 490 1 8 HELIX 14 AB5 GLY B 192 ASP B 196 1 5 HELIX 15 AB6 ARG B 243 LEU B 251 1 9 HELIX 16 AB7 ASP B 280 GLY B 289 1 10 HELIX 17 AB8 GLY B 292 MET B 313 1 22 HELIX 18 AB9 THR B 358 VAL B 362 5 5 HELIX 19 AC1 ALA B 363 ILE B 367 5 5 HELIX 20 AC2 TYR B 385 GLY B 404 1 20 HELIX 21 AC3 ASP B 414 ARG B 422 1 9 HELIX 22 AC4 HIS B 426 PHE B 433 1 8 HELIX 23 AC5 SER B 436 LEU B 447 1 12 HELIX 24 AC6 THR B 456 ASN B 462 1 7 HELIX 25 AC7 HIS B 463 MET B 468 1 6 HELIX 26 AC8 SER B 483 LEU B 494 1 12 SHEET 1 AA1 5 PHE A 197 ILE A 200 0 SHEET 2 AA1 5 VAL A 212 GLU A 217 -1 O ILE A 216 N SER A 198 SHEET 3 AA1 5 THR A 223 ILE A 229 -1 O VAL A 226 N LYS A 213 SHEET 4 AA1 5 TYR A 269 GLU A 274 -1 O MET A 271 N LYS A 227 SHEET 5 AA1 5 LEU A 259 TYR A 263 -1 N TYR A 263 O TYR A 270 SHEET 1 AA2 2 ILE A 325 GLN A 329 0 SHEET 2 AA2 2 LEU A 334 ILE A 337 -1 O LYS A 336 N LEU A 326 SHEET 1 AA3 6 GLY A 477 ASP A 478 0 SHEET 2 AA3 6 LEU B 259 PHE B 262 -1 O PHE B 262 N GLY A 477 SHEET 3 AA3 6 TYR B 270 GLU B 274 -1 O VAL B 272 N GLY B 261 SHEET 4 AA3 6 THR B 223 ILE B 228 -1 N LYS B 227 O MET B 271 SHEET 5 AA3 6 THR B 211 GLU B 217 -1 N THR B 211 O ILE B 228 SHEET 6 AA3 6 PHE B 197 ILE B 199 -1 N SER B 198 O ILE B 216 SHEET 1 AA4 2 ILE B 325 GLN B 329 0 SHEET 2 AA4 2 LEU B 334 ILE B 337 -1 O LYS B 336 N LEU B 326 CISPEP 1 THR B 191 GLY B 192 0 -2.09 SITE 1 AC1 9 VAL A 212 SER A 225 MET A 273 GLU A 274 SITE 2 AC1 9 VAL A 276 ASP A 280 ASP A 323 ASN A 324 SITE 3 AC1 9 LEU A 326 SITE 1 AC2 8 SER B 225 MET B 273 GLU B 274 VAL B 276 SITE 2 AC2 8 ASP B 280 ASP B 323 ASN B 324 LEU B 326 CRYST1 74.149 77.539 222.170 90.00 90.00 90.00 C 2 2 21 16 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 0.013486 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012897 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004501 0.00000