HEADER TRANSFERASE 14-FEB-14 4OTP TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF THE HUMAN RIOK1 ATYPICAL TITLE 2 PROTEIN KINASE IN COMPLEX WITH ADP/MG2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE RIO1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RIO DOMAIN (UNP RESIDUES 143-494); COMPND 5 SYNONYM: RIOK1, RIO KINASE 1; COMPND 6 EC: 2.7.11.1; 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: RIOK1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ATYPICAL KINASE DOMAIN, RIO DOMAIN, RIBOSOME BIOGENESIS, PRE-40S, KEYWDS 2 PRERIBOSOME, PHOSPHORYLATION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR N.A.LARONDE,I.N.KIBURU REVDAT 2 13-AUG-14 4OTP 1 JRNL REVDAT 1 02-JUL-14 4OTP 0 JRNL AUTH S.FERREIRA-CERCA,I.KIBURU,E.THOMSON,N.LARONDE,E.HURT JRNL TITL DOMINANT RIO1 KINASE/ATPASE CATALYTIC MUTANT INDUCES JRNL TITL 2 TRAPPING OF LATE PRE-40S BIOGENESIS FACTORS IN 80S-LIKE JRNL TITL 3 RIBOSOMES. JRNL REF NUCLEIC ACIDS RES. V. 42 8635 2014 JRNL REFN ISSN 0305-1048 JRNL PMID 24948609 JRNL DOI 10.1093/NAR/GKU542 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 10668 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.150 REMARK 3 FREE R VALUE TEST SET COUNT : 1083 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 42.9542 - 5.3970 1.00 1368 147 0.1917 0.1980 REMARK 3 2 5.3970 - 4.2850 1.00 1281 142 0.1658 0.2098 REMARK 3 3 4.2850 - 3.7437 0.99 1263 143 0.1713 0.2045 REMARK 3 4 3.7437 - 3.4016 0.98 1247 137 0.2107 0.3155 REMARK 3 5 3.4016 - 3.1578 0.96 1193 133 0.2548 0.2849 REMARK 3 6 3.1578 - 2.9717 0.91 1148 134 0.2766 0.3575 REMARK 3 7 2.9717 - 2.8229 0.88 1080 130 0.2853 0.3439 REMARK 3 8 2.8229 - 2.7000 0.80 1005 117 0.3161 0.3448 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 58.88 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 : 0.014 1956 REMARK 3 ANGLE : 1.300 2635 REMARK 3 CHIRALITY : 0.080 291 REMARK 3 PLANARITY : 0.004 334 REMARK 3 DIHEDRAL : 20.095 742 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 163 through 175 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.0271 46.4999 6.6526 REMARK 3 T TENSOR REMARK 3 T11: 2.0473 T22: 1.6523 REMARK 3 T33: 0.6226 T12: 0.1458 REMARK 3 T13: -0.1014 T23: 0.1180 REMARK 3 L TENSOR REMARK 3 L11: 7.4257 L22: 6.1168 REMARK 3 L33: 3.6075 L12: 4.1272 REMARK 3 L13: 4.1832 L23: 3.6541 REMARK 3 S TENSOR REMARK 3 S11: -0.5445 S12: 1.5760 S13: 0.4925 REMARK 3 S21: 0.2216 S22: 0.5445 S23: 0.3763 REMARK 3 S31: 0.3967 S32: 2.1760 S33: 0.0912 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: chain 'A' and (resid 176 through 245 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.4648 44.5941 16.9876 REMARK 3 T TENSOR REMARK 3 T11: 1.4763 T22: 1.1144 REMARK 3 T33: 0.5315 T12: 0.2971 REMARK 3 T13: -0.0316 T23: -0.0298 REMARK 3 L TENSOR REMARK 3 L11: 3.1453 L22: 2.1471 REMARK 3 L33: 3.3904 L12: 0.2085 REMARK 3 L13: 0.3644 L23: -1.4857 REMARK 3 S TENSOR REMARK 3 S11: -0.6021 S12: 0.2229 S13: 0.2108 REMARK 3 S21: -0.2468 S22: 0.3175 S23: 0.0823 REMARK 3 S31: -0.9250 S32: -0.0763 S33: 0.2731 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: chain 'A' and (resid 246 through 277 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.3058 32.4742 20.1483 REMARK 3 T TENSOR REMARK 3 T11: 1.2610 T22: 0.9792 REMARK 3 T33: 0.4761 T12: 0.5235 REMARK 3 T13: -0.1423 T23: -0.3009 REMARK 3 L TENSOR REMARK 3 L11: 2.1463 L22: 3.6327 REMARK 3 L33: 3.2304 L12: -1.6033 REMARK 3 L13: 1.0824 L23: -0.0343 REMARK 3 S TENSOR REMARK 3 S11: 0.2691 S12: 0.3857 S13: 0.4172 REMARK 3 S21: -0.9025 S22: -0.3888 S23: -0.2427 REMARK 3 S31: -0.2024 S32: 0.7586 S33: -1.7292 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: chain 'A' and (resid 278 through 352 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.1727 33.6810 34.7157 REMARK 3 T TENSOR REMARK 3 T11: 1.0864 T22: 0.8586 REMARK 3 T33: 0.6043 T12: 0.4442 REMARK 3 T13: -0.1532 T23: -0.1052 REMARK 3 L TENSOR REMARK 3 L11: 1.6459 L22: 2.3391 REMARK 3 L33: 4.0822 L12: 0.4801 REMARK 3 L13: 0.1842 L23: 0.3805 REMARK 3 S TENSOR REMARK 3 S11: 0.4291 S12: 0.4136 S13: -0.4132 REMARK 3 S21: -0.6338 S22: -0.1982 S23: 0.3939 REMARK 3 S31: 0.3299 S32: 0.2003 S33: -0.1268 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: chain 'A' and (resid 353 through 371 ) REMARK 3 ORIGIN FOR THE GROUP (A): 33.7561 34.4934 43.4232 REMARK 3 T TENSOR REMARK 3 T11: 0.8530 T22: 1.1059 REMARK 3 T33: 0.5488 T12: 0.2643 REMARK 3 T13: -0.1775 T23: -0.1380 REMARK 3 L TENSOR REMARK 3 L11: 4.6234 L22: 3.5915 REMARK 3 L33: 2.9263 L12: -3.0296 REMARK 3 L13: 0.0653 L23: -1.6932 REMARK 3 S TENSOR REMARK 3 S11: -0.2269 S12: -0.4816 S13: 0.6149 REMARK 3 S21: 0.0279 S22: 0.1467 S23: -0.2736 REMARK 3 S31: -0.9095 S32: 1.5159 S33: 0.4979 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: chain 'A' and (resid 372 through 410 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.5610 22.3415 48.3913 REMARK 3 T TENSOR REMARK 3 T11: 0.9192 T22: 0.5350 REMARK 3 T33: 0.6522 T12: 0.3146 REMARK 3 T13: -0.1812 T23: -0.0261 REMARK 3 L TENSOR REMARK 3 L11: 6.1882 L22: 4.0840 REMARK 3 L33: 1.8071 L12: -1.5176 REMARK 3 L13: -0.4054 L23: 2.4530 REMARK 3 S TENSOR REMARK 3 S11: -0.0871 S12: -0.5760 S13: -0.6311 REMARK 3 S21: 0.2818 S22: -0.1297 S23: 0.3065 REMARK 3 S31: 1.3055 S32: 0.3410 S33: -0.0720 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: chain 'A' and (resid 411 through 430 ) REMARK 3 ORIGIN FOR THE GROUP (A): 42.0147 31.3743 52.6730 REMARK 3 T TENSOR REMARK 3 T11: 0.8845 T22: 1.2356 REMARK 3 T33: 0.5665 T12: 0.2620 REMARK 3 T13: -0.0129 T23: 0.1244 REMARK 3 L TENSOR REMARK 3 L11: 9.1627 L22: 4.1065 REMARK 3 L33: 6.4756 L12: -3.4353 REMARK 3 L13: -7.2726 L23: 2.9855 REMARK 3 S TENSOR REMARK 3 S11: 0.7732 S12: 0.1127 S13: 1.6286 REMARK 3 S21: -0.5446 S22: -0.1225 S23: -0.4723 REMARK 3 S31: -1.4057 S32: 0.1849 S33: -0.0662 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 4OTP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-FEB-14. REMARK 100 THE RCSB ID CODE IS RCSB084935. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : KOHZU HLD8-24 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11336 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 42.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.6900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.21500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% PEG400, 0.1 M HEPES, PH 7.5, 0.2 M REMARK 280 CALCIUM CHLORIDE, VAPOR DIFFUSION, 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 73.71333 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 36.85667 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 36.85667 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 73.71333 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 GLU A 143 REMARK 465 ALA A 144 REMARK 465 ASP A 145 REMARK 465 MSE A 146 REMARK 465 TYR A 147 REMARK 465 ARG A 148 REMARK 465 ILE A 149 REMARK 465 LYS A 150 REMARK 465 ASP A 151 REMARK 465 LYS A 152 REMARK 465 ALA A 153 REMARK 465 ASP A 154 REMARK 465 ARG A 155 REMARK 465 ALA A 156 REMARK 465 THR A 157 REMARK 465 VAL A 158 REMARK 465 GLU A 159 REMARK 465 GLN A 160 REMARK 465 VAL A 161 REMARK 465 LEU A 162 REMARK 465 THR A 212 REMARK 465 SER A 213 REMARK 465 ILE A 214 REMARK 465 LEU A 215 REMARK 465 VAL A 216 REMARK 465 PHE A 217 REMARK 465 LYS A 218 REMARK 465 ASP A 219 REMARK 465 ARG A 220 REMARK 465 ASP A 221 REMARK 465 LYS A 222 REMARK 465 TYR A 223 REMARK 465 VAL A 224 REMARK 465 SER A 225 REMARK 465 GLY A 226 REMARK 465 GLU A 227 REMARK 465 PHE A 228 REMARK 465 ARG A 229 REMARK 465 PHE A 230 REMARK 465 ARG A 231 REMARK 465 HIS A 232 REMARK 465 GLY A 233 REMARK 465 TYR A 234 REMARK 465 CYS A 235 REMARK 465 LYS A 236 REMARK 465 GLY A 237 REMARK 465 ASN A 238 REMARK 465 PRO A 239 REMARK 465 ARG A 240 REMARK 465 LYS A 241 REMARK 465 MSE A 242 REMARK 465 VAL A 243 REMARK 465 PRO A 431 REMARK 465 ARG A 432 REMARK 465 THR A 433 REMARK 465 LEU A 434 REMARK 465 ASN A 435 REMARK 465 GLU A 436 REMARK 465 VAL A 437 REMARK 465 LYS A 438 REMARK 465 ASN A 439 REMARK 465 TYR A 440 REMARK 465 GLU A 441 REMARK 465 ARG A 442 REMARK 465 ASP A 443 REMARK 465 MSE A 444 REMARK 465 ASP A 445 REMARK 465 ILE A 446 REMARK 465 ILE A 447 REMARK 465 MSE A 448 REMARK 465 LYS A 449 REMARK 465 LEU A 450 REMARK 465 LYS A 451 REMARK 465 GLU A 452 REMARK 465 GLU A 453 REMARK 465 ASP A 454 REMARK 465 MSE A 455 REMARK 465 ALA A 456 REMARK 465 MSE A 457 REMARK 465 ASN A 458 REMARK 465 ALA A 459 REMARK 465 GLN A 460 REMARK 465 GLN A 461 REMARK 465 ASP A 462 REMARK 465 ASN A 463 REMARK 465 ILE A 464 REMARK 465 LEU A 465 REMARK 465 TYR A 466 REMARK 465 GLN A 467 REMARK 465 THR A 468 REMARK 465 VAL A 469 REMARK 465 THR A 470 REMARK 465 GLY A 471 REMARK 465 LEU A 472 REMARK 465 LYS A 473 REMARK 465 LYS A 474 REMARK 465 ASP A 475 REMARK 465 LEU A 476 REMARK 465 SER A 477 REMARK 465 GLY A 478 REMARK 465 VAL A 479 REMARK 465 GLN A 480 REMARK 465 LYS A 481 REMARK 465 VAL A 482 REMARK 465 PRO A 483 REMARK 465 ALA A 484 REMARK 465 LEU A 485 REMARK 465 LEU A 486 REMARK 465 GLU A 487 REMARK 465 ASN A 488 REMARK 465 GLN A 489 REMARK 465 VAL A 490 REMARK 465 GLU A 491 REMARK 465 GLU A 492 REMARK 465 ARG A 493 REMARK 465 THR A 494 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 ASP A 163 CG OD1 OD2 REMARK 470 PRO A 164 CG CD REMARK 470 LYS A 190 CG CD CE NZ REMARK 470 LYS A 244 CG CD CE NZ REMARK 470 THR A 245 OG1 CG2 REMARK 470 PRO A 351 CG CD REMARK 470 TYR A 429 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ILE A 430 CG1 CG2 CD1 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 O3B ADP A 501 O HOH A 604 2.00 REMARK 500 O3B ADP A 501 O HOH A 602 2.18 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 PRO A 164 N - CA - CB ANGL. DEV. = 7.2 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 PRO A 164 8.19 -68.74 REMARK 500 THR A 180 -75.06 -66.64 REMARK 500 ASN A 201 38.35 -88.89 REMARK 500 SER A 272 -118.87 55.60 REMARK 500 ASP A 283 -138.48 47.89 REMARK 500 ASN A 292 42.64 -100.17 REMARK 500 ASP A 317 -65.41 -97.73 REMARK 500 ASP A 324 42.15 -154.37 REMARK 500 PHD A 341 70.90 63.63 REMARK 500 HIS A 348 -31.14 -33.84 REMARK 500 PRO A 388 72.71 -61.73 REMARK 500 SER A 389 93.41 -171.36 REMARK 500 THR A 391 -13.43 53.45 REMARK 500 HIS A 392 -55.71 41.17 REMARK 500 TYR A 429 86.59 -162.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP A 501 O2A REMARK 620 2 HOH A 602 O 122.5 REMARK 620 3 HOH A 603 O 94.4 123.9 REMARK 620 4 ASN A 329 OD1 109.8 114.3 84.9 REMARK 620 5 ADP A 501 O3B 72.5 56.5 108.6 166.2 REMARK 620 6 PHD A 341 OD1 72.3 69.9 165.3 93.7 73.9 REMARK 620 7 HOH A 604 O 96.6 63.7 72.3 146.4 42.6 114.6 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 502 DBREF 4OTP A 143 494 UNP Q9BRS2 RIOK1_HUMAN 143 494 SEQRES 1 A 352 GLU ALA ASP MSE TYR ARG ILE LYS ASP LYS ALA ASP ARG SEQRES 2 A 352 ALA THR VAL GLU GLN VAL LEU ASP PRO ARG THR ARG MSE SEQRES 3 A 352 ILE LEU PHE LYS MSE LEU THR ARG GLY ILE ILE THR GLU SEQRES 4 A 352 ILE ASN GLY CYS ILE SER THR GLY LYS GLU ALA ASN VAL SEQRES 5 A 352 TYR HIS ALA SER THR ALA ASN GLY GLU SER ARG ALA ILE SEQRES 6 A 352 LYS ILE TYR LYS THR SER ILE LEU VAL PHE LYS ASP ARG SEQRES 7 A 352 ASP LYS TYR VAL SER GLY GLU PHE ARG PHE ARG HIS GLY SEQRES 8 A 352 TYR CYS LYS GLY ASN PRO ARG LYS MSE VAL LYS THR TRP SEQRES 9 A 352 ALA GLU LYS GLU MSE ARG ASN LEU ILE ARG LEU ASN THR SEQRES 10 A 352 ALA GLU ILE PRO CYS PRO GLU PRO ILE MET LEU ARG SER SEQRES 11 A 352 HIS VAL LEU VAL MSE SER PHE ILE GLY LYS ASP ASP MSE SEQRES 12 A 352 PRO ALA PRO LEU LEU LYS ASN VAL GLN LEU SER GLU SER SEQRES 13 A 352 LYS ALA ARG GLU LEU TYR LEU GLN VAL ILE GLN TYR MSE SEQRES 14 A 352 ARG ARG MSE TYR GLN ASP ALA ARG LEU VAL HIS ALA ASP SEQRES 15 A 352 LEU SER GLU PHE ASN MSE LEU TYR HIS GLY GLY GLY VAL SEQRES 16 A 352 TYR ILE ILE PHD VAL SER GLN SER VAL GLU HIS ASP HIS SEQRES 17 A 352 PRO HIS ALA LEU GLU PHE LEU ARG LYS ASP CYS ALA ASN SEQRES 18 A 352 VAL ASN ASP PHE PHE MSE ARG HIS SER VAL ALA VAL MSE SEQRES 19 A 352 THR VAL ARG GLU LEU PHE GLU PHE VAL THR ASP PRO SER SEQRES 20 A 352 ILE THR HIS GLU ASN MET ASP ALA TYR LEU SER LYS ALA SEQRES 21 A 352 MSE GLU ILE ALA SER GLN ARG THR LYS GLU GLU ARG SER SEQRES 22 A 352 SER GLN ASP HIS VAL ASP GLU GLU VAL PHE LYS ARG ALA SEQRES 23 A 352 TYR ILE PRO ARG THR LEU ASN GLU VAL LYS ASN TYR GLU SEQRES 24 A 352 ARG ASP MSE ASP ILE ILE MSE LYS LEU LYS GLU GLU ASP SEQRES 25 A 352 MSE ALA MSE ASN ALA GLN GLN ASP ASN ILE LEU TYR GLN SEQRES 26 A 352 THR VAL THR GLY LEU LYS LYS ASP LEU SER GLY VAL GLN SEQRES 27 A 352 LYS VAL PRO ALA LEU LEU GLU ASN GLN VAL GLU GLU ARG SEQRES 28 A 352 THR MODRES 4OTP MSE A 168 MET SELENOMETHIONINE MODRES 4OTP MSE A 173 MET SELENOMETHIONINE MODRES 4OTP MSE A 251 MET SELENOMETHIONINE MODRES 4OTP MSE A 277 MET SELENOMETHIONINE MODRES 4OTP MSE A 285 MET SELENOMETHIONINE MODRES 4OTP MSE A 311 MET SELENOMETHIONINE MODRES 4OTP MSE A 314 MET SELENOMETHIONINE MODRES 4OTP MSE A 330 MET SELENOMETHIONINE MODRES 4OTP PHD A 341 ASP ASPARTYL PHOSPHATE MODRES 4OTP MSE A 369 MET SELENOMETHIONINE MODRES 4OTP MSE A 376 MET SELENOMETHIONINE MODRES 4OTP MSE A 403 MET SELENOMETHIONINE HET MSE A 168 8 HET MSE A 173 8 HET MSE A 251 8 HET MSE A 277 8 HET MSE A 285 8 HET MSE A 311 8 HET MSE A 314 8 HET MSE A 330 8 HET PHD A 341 12 HET MSE A 369 8 HET MSE A 376 8 HET MSE A 403 8 HET ADP A 501 27 HET MG A 502 1 HETNAM MSE SELENOMETHIONINE HETNAM PHD ASPARTYL PHOSPHATE HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 1 MSE 11(C5 H11 N O2 SE) FORMUL 1 PHD C4 H8 N O7 P FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 MG MG 2+ FORMUL 4 HOH *7(H2 O) HELIX 1 1 ARG A 165 ARG A 176 1 12 HELIX 2 2 THR A 245 ALA A 260 1 16 HELIX 3 3 LEU A 289 VAL A 293 5 5 HELIX 4 4 SER A 296 ASP A 317 1 22 HELIX 5 5 SER A 326 PHE A 328 5 3 HELIX 6 6 HIS A 352 ARG A 370 1 19 HELIX 7 7 THR A 377 ASP A 387 1 11 HELIX 8 8 ASN A 394 ARG A 409 1 16 HELIX 9 9 THR A 410 TYR A 429 1 20 SHEET 1 A 5 GLU A 181 THR A 188 0 SHEET 2 A 5 ALA A 192 SER A 198 -1 O SER A 198 N GLU A 181 SHEET 3 A 5 SER A 204 TYR A 210 -1 O ILE A 209 N ASN A 193 SHEET 4 A 5 VAL A 274 SER A 278 -1 O LEU A 275 N LYS A 208 SHEET 5 A 5 PRO A 267 ARG A 271 -1 N MET A 269 O VAL A 276 SHEET 1 B 2 GLY A 281 LYS A 282 0 SHEET 2 B 2 MSE A 285 PRO A 286 -1 O MSE A 285 N LYS A 282 SHEET 1 C 2 LEU A 320 VAL A 321 0 SHEET 2 C 2 VAL A 346 GLU A 347 -1 O VAL A 346 N VAL A 321 SHEET 1 D 2 MSE A 330 HIS A 333 0 SHEET 2 D 2 GLY A 336 ILE A 339 -1 O TYR A 338 N LEU A 331 LINK C ARG A 167 N MSE A 168 1555 1555 1.33 LINK C MSE A 168 N ILE A 169 1555 1555 1.33 LINK C LYS A 172 N MSE A 173 1555 1555 1.32 LINK C MSE A 173 N LEU A 174 1555 1555 1.32 LINK C GLU A 250 N MSE A 251 1555 1555 1.33 LINK C MSE A 251 N ARG A 252 1555 1555 1.33 LINK C VAL A 276 N MSE A 277 1555 1555 1.32 LINK C MSE A 277 N SER A 278 1555 1555 1.33 LINK C ASP A 284 N MSE A 285 1555 1555 1.34 LINK C MSE A 285 N PRO A 286 1555 1555 1.33 LINK C TYR A 310 N MSE A 311 1555 1555 1.33 LINK C MSE A 311 N ARG A 312 1555 1555 1.33 LINK C ARG A 313 N MSE A 314 1555 1555 1.32 LINK C MSE A 314 N TYR A 315 1555 1555 1.33 LINK C ASN A 329 N MSE A 330 1555 1555 1.33 LINK C MSE A 330 N LEU A 331 1555 1555 1.32 LINK C ILE A 340 N PHD A 341 1555 1555 1.33 LINK C PHD A 341 N VAL A 342 1555 1555 1.33 LINK C PHE A 368 N MSE A 369 1555 1555 1.32 LINK C MSE A 369 N ARG A 370 1555 1555 1.33 LINK C VAL A 375 N MSE A 376 1555 1555 1.33 LINK C MSE A 376 N THR A 377 1555 1555 1.33 LINK C ALA A 402 N MSE A 403 1555 1555 1.33 LINK C MSE A 403 N GLU A 404 1555 1555 1.33 LINK O2A ADP A 501 MG MG A 502 1555 1555 1.79 LINK MG MG A 502 O HOH A 602 1555 1555 2.05 LINK MG MG A 502 O HOH A 603 1555 1555 2.11 LINK OD1 ASN A 329 MG MG A 502 1555 1555 2.13 LINK O3B ADP A 501 MG MG A 502 1555 1555 2.49 LINK OD1 PHD A 341 MG MG A 502 1555 1555 2.88 LINK MG MG A 502 O HOH A 604 1555 1555 2.92 CISPEP 1 GLY A 334 GLY A 335 0 -6.51 SITE 1 AC1 16 ILE A 186 SER A 187 VAL A 194 LYS A 208 SITE 2 AC1 16 PRO A 265 MSE A 277 SER A 278 ILE A 280 SITE 3 AC1 16 LEU A 289 ASN A 329 ILE A 340 PHD A 341 SITE 4 AC1 16 MG A 502 HOH A 602 HOH A 603 HOH A 604 SITE 1 AC2 6 ASN A 329 PHD A 341 ADP A 501 HOH A 602 SITE 2 AC2 6 HOH A 603 HOH A 604 CRYST1 78.760 78.760 110.570 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 0.012697 0.007331 0.000000 0.00000 SCALE2 0.000000 0.014661 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009044 0.00000