HEADER TRANSFERASE 05-SEP-12 4GYI TITLE CRYSTAL STRUCTURE OF THE RIO2 KINASE-ADP/MG2+-PHOSPHOASPARTATE COMPLEX TITLE 2 FROM CHAETOMIUM THERMOPHILUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIO2 KINASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHAETOMIUM THERMOPHILUM; SOURCE 3 ORGANISM_TAXID: 759272; SOURCE 4 STRAIN: DSM 1495 / CBS 144.50 / IMI 039719; SOURCE 5 GENE: CTHT_0033330, RIO2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA(TM) PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PT7 KEYWDS PROTEIN KINASE, ADP COMPLEX, PHOSPHOASPARTATE, ACYL-PHOSPHATE, KEYWDS 2 RIBOSOME BIOGENESIS, SER/THR PROTEIN KINASE, RIBOSOME BIOGENESIS; KEYWDS 3 RIBOSOMAL RNA PROCESSING; PRE-40S MATURATION, PRE-40S, KEYWDS 4 PHOSPHORYLATION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.FERREIRA-CERCA,V.SAGAR,T.SCHAFER,M.DIOP,A.M.WESSELING,H.LU,E.CHAI, AUTHOR 2 E.HURT,N.LARONDE-LEBLANC REVDAT 4 13-SEP-23 4GYI 1 REMARK SEQADV LINK REVDAT 3 26-DEC-12 4GYI 1 JRNL REVDAT 2 12-DEC-12 4GYI 1 JRNL REVDAT 1 17-OCT-12 4GYI 0 JRNL AUTH S.FERREIRA-CERCA,V.SAGAR,T.SCHAFER,M.DIOP,A.M.WESSELING, JRNL AUTH 2 H.LU,E.CHAI,E.HURT,N.LARONDE-LEBLANC JRNL TITL ATPASE-DEPENDENT ROLE OF THE ATYPICAL KINASE RIO2 ON THE JRNL TITL 2 EVOLVING PRE-40S RIBOSOMAL SUBUNIT. JRNL REF NAT.STRUCT.MOL.BIOL. V. 19 1316 2012 JRNL REFN ISSN 1545-9993 JRNL PMID 23104056 JRNL DOI 10.1038/NSMB.2403 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.130 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 18535 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.140 REMARK 3 FREE R VALUE TEST SET COUNT : 1880 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 34.5367 - 5.1672 0.99 1334 152 0.1562 0.1799 REMARK 3 2 5.1672 - 4.1035 1.00 1362 142 0.1277 0.1943 REMARK 3 3 4.1035 - 3.5854 1.00 1344 147 0.1653 0.1996 REMARK 3 4 3.5854 - 3.2579 0.99 1343 152 0.1740 0.2419 REMARK 3 5 3.2579 - 3.0245 0.98 1326 140 0.1727 0.2565 REMARK 3 6 3.0245 - 2.8463 0.98 1311 153 0.1858 0.2615 REMARK 3 7 2.8463 - 2.7038 0.97 1292 155 0.1977 0.2557 REMARK 3 8 2.7038 - 2.5862 0.96 1289 159 0.1924 0.2556 REMARK 3 9 2.5862 - 2.4866 0.94 1247 136 0.2123 0.2793 REMARK 3 10 2.4866 - 2.4008 0.92 1238 140 0.1958 0.2936 REMARK 3 11 2.4008 - 2.3258 0.91 1229 139 0.2095 0.3141 REMARK 3 12 2.3258 - 2.2593 0.89 1190 136 0.1967 0.2934 REMARK 3 13 2.2593 - 2.1998 0.85 1150 129 0.2056 0.2376 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.33 REMARK 3 B_SOL : 46.95 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.55 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.83810 REMARK 3 B22 (A**2) : 1.83810 REMARK 3 B33 (A**2) : -3.67610 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 2791 REMARK 3 ANGLE : 1.214 3773 REMARK 3 CHIRALITY : 0.078 414 REMARK 3 PLANARITY : 0.005 476 REMARK 3 DIHEDRAL : 15.794 1064 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 2:76 ) REMARK 3 ORIGIN FOR THE GROUP (A): 42.5519 15.2265 -32.8661 REMARK 3 T TENSOR REMARK 3 T11: 0.3166 T22: 0.5805 REMARK 3 T33: 0.3579 T12: 0.2759 REMARK 3 T13: 0.0208 T23: -0.0774 REMARK 3 L TENSOR REMARK 3 L11: 5.6126 L22: 4.3229 REMARK 3 L33: 3.0259 L12: -1.9815 REMARK 3 L13: -1.2259 L23: 0.7070 REMARK 3 S TENSOR REMARK 3 S11: 0.0917 S12: 0.2885 S13: 0.0902 REMARK 3 S21: -0.0637 S22: 0.0143 S23: -0.5962 REMARK 3 S31: 0.1795 S32: 0.4959 S33: -0.0584 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 77:176 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.3474 20.1477 -27.6501 REMARK 3 T TENSOR REMARK 3 T11: 0.2729 T22: 0.1112 REMARK 3 T33: 0.2629 T12: 0.0984 REMARK 3 T13: 0.0020 T23: -0.0228 REMARK 3 L TENSOR REMARK 3 L11: 2.9452 L22: 0.2262 REMARK 3 L33: 2.7613 L12: 0.4282 REMARK 3 L13: 0.7800 L23: 0.1707 REMARK 3 S TENSOR REMARK 3 S11: 0.0418 S12: 0.1853 S13: -0.0141 REMARK 3 S21: -0.1478 S22: -0.0397 S23: 0.0137 REMARK 3 S31: 0.2336 S32: 0.2138 S33: 0.0069 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 177:321 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.6098 21.7678 -17.4982 REMARK 3 T TENSOR REMARK 3 T11: 0.2109 T22: 0.2249 REMARK 3 T33: 0.2786 T12: -0.0442 REMARK 3 T13: 0.0197 T23: 0.0173 REMARK 3 L TENSOR REMARK 3 L11: 3.3677 L22: 1.7005 REMARK 3 L33: 3.3399 L12: -0.0761 REMARK 3 L13: -0.3678 L23: 0.2757 REMARK 3 S TENSOR REMARK 3 S11: 0.1160 S12: -0.3690 S13: -0.0047 REMARK 3 S21: 0.1289 S22: 0.0329 S23: 0.3044 REMARK 3 S31: 0.0965 S32: -0.5625 S33: -0.0925 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 322:341 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.1423 20.1775 -11.1522 REMARK 3 T TENSOR REMARK 3 T11: 0.3803 T22: 0.3754 REMARK 3 T33: 0.3480 T12: 0.0525 REMARK 3 T13: 0.0515 T23: -0.0548 REMARK 3 L TENSOR REMARK 3 L11: 8.3609 L22: 4.7206 REMARK 3 L33: 8.7872 L12: -5.7383 REMARK 3 L13: 1.9543 L23: -1.5331 REMARK 3 S TENSOR REMARK 3 S11: -0.4425 S12: -0.6635 S13: 0.4236 REMARK 3 S21: 1.7319 S22: 0.5256 S23: 0.2789 REMARK 3 S31: -0.2513 S32: -0.7039 S33: -0.0242 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 4GYI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000074792. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19451 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06700 REMARK 200 FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.07960 REMARK 200 R SYM FOR SHELL (I) : 0.14400 REMARK 200 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: PHENIX REMARK 200 STARTING MODEL: 1TQP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS, 14-16% POLY-ETHYLENE REMARK 280 GLYCOL, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 59.81200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.53247 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 23.92767 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 59.81200 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 34.53247 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 23.92767 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 59.81200 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 34.53247 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 23.92767 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 69.06495 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 47.85533 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 69.06495 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 47.85533 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 69.06495 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 47.85533 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 SER A 0 REMARK 465 MET A 1 REMARK 465 ALA A 138 REMARK 465 ASN A 139 REMARK 465 ASN A 343 REMARK 465 ASP A 344 REMARK 465 GLU A 345 REMARK 465 GLU A 346 REMARK 465 ASP A 347 REMARK 465 SER A 348 REMARK 465 ASP A 349 REMARK 465 ASP A 350 REMARK 465 TYR A 351 REMARK 465 GLU A 352 REMARK 465 GLU A 353 REMARK 465 ASP A 354 REMARK 465 SER A 355 REMARK 465 ASP A 356 REMARK 465 LYS A 357 REMARK 465 GLU A 358 REMARK 465 LYS A 359 REMARK 465 ALA A 360 REMARK 465 SER A 361 REMARK 465 ASN A 362 REMARK 465 GLU A 363 REMARK 465 ASP A 364 REMARK 465 THR A 365 REMARK 465 ASP A 366 REMARK 465 VAL A 367 REMARK 465 ASP A 368 REMARK 465 ASP A 369 REMARK 465 GLY A 370 REMARK 465 ARG A 371 REMARK 465 LEU A 372 REMARK 465 GLN A 373 REMARK 465 VAL A 374 REMARK 465 ILE A 375 REMARK 465 GLY A 376 REMARK 465 ASP A 377 REMARK 465 HIS A 378 REMARK 465 VAL A 379 REMARK 465 GLN A 380 REMARK 465 LEU A 381 REMARK 465 GLY A 382 REMARK 465 THR A 383 REMARK 465 GLU A 384 REMARK 465 GLY A 385 REMARK 465 ASP A 386 REMARK 465 LEU A 387 REMARK 465 LYS A 388 REMARK 465 LYS A 389 REMARK 465 LEU A 390 REMARK 465 THR A 391 REMARK 465 ILE A 392 REMARK 465 ASN A 393 REMARK 465 ASP A 394 REMARK 465 GLY A 395 REMARK 465 THR A 396 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 LYS A 2 CG CD CE NZ REMARK 470 ASN A 28 CG OD1 ND2 REMARK 470 LYS A 67 CG CD CE NZ REMARK 470 LYS A 137 CG CD CE NZ REMARK 470 ARG A 140 CG CD NE CZ NH1 NH2 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 OE1 GLU A 107 O HOH A 509 2.11 REMARK 500 O HOH A 533 O HOH A 584 2.13 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 ASN A 28 -65.07 -90.62 REMARK 500 ARG A 184 -119.08 54.32 REMARK 500 ASP A 229 47.31 -147.71 REMARK 500 PHD A 257 83.44 78.16 REMARK 500 ASP A 309 -141.24 61.08 REMARK 500 ALA A 311 104.72 -48.49 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 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 234 OD1 REMARK 620 2 PHD A 257 OD1 106.5 REMARK 620 3 ADP A 401 O1A 94.5 95.4 REMARK 620 4 ADP A 401 O2B 165.7 87.0 79.1 REMARK 620 5 HOH A 523 O 81.7 171.7 85.2 85.0 REMARK 620 6 HOH A 543 O 96.4 92.3 164.3 87.6 85.2 REMARK 620 N 1 2 3 4 5 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GYG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF APO-RIO2 KINASE FROM C. THERMOPHILUM REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE AS PROVIDED, INCLUDING RESIDUES 1-23 IS THE CORRECT REMARK 999 SEQUENCE OF THE PROTEIN. THE UNIPROT DATABASE HAVE BEEN NOTIFIED OF REMARK 999 THE ERROR DBREF 4GYI A 24 396 UNP G0S5R3 G0S5R3_CHATD 1 373 SEQADV 4GYI SER A 0 UNP G0S5R3 EXPRESSION TAG SEQADV 4GYI MET A 1 UNP G0S5R3 SEE REMARK 999 SEQADV 4GYI LYS A 2 UNP G0S5R3 SEE REMARK 999 SEQADV 4GYI LEU A 3 UNP G0S5R3 SEE REMARK 999 SEQADV 4GYI ASP A 4 UNP G0S5R3 SEE REMARK 999 SEQADV 4GYI THR A 5 UNP G0S5R3 SEE REMARK 999 SEQADV 4GYI ARG A 6 UNP G0S5R3 SEE REMARK 999 SEQADV 4GYI ALA A 7 UNP G0S5R3 SEE REMARK 999 SEQADV 4GYI MET A 8 UNP G0S5R3 SEE REMARK 999 SEQADV 4GYI ARG A 9 UNP G0S5R3 SEE REMARK 999 SEQADV 4GYI HIS A 10 UNP G0S5R3 SEE REMARK 999 SEQADV 4GYI LEU A 11 UNP G0S5R3 SEE REMARK 999 SEQADV 4GYI THR A 12 UNP G0S5R3 SEE REMARK 999 SEQADV 4GYI ALA A 13 UNP G0S5R3 SEE REMARK 999 SEQADV 4GYI GLU A 14 UNP G0S5R3 SEE REMARK 999 SEQADV 4GYI ASP A 15 UNP G0S5R3 SEE REMARK 999 SEQADV 4GYI TRP A 16 UNP G0S5R3 SEE REMARK 999 SEQADV 4GYI ARG A 17 UNP G0S5R3 SEE REMARK 999 SEQADV 4GYI VAL A 18 UNP G0S5R3 SEE REMARK 999 SEQADV 4GYI LEU A 19 UNP G0S5R3 SEE REMARK 999 SEQADV 4GYI THR A 20 UNP G0S5R3 SEE REMARK 999 SEQADV 4GYI ALA A 21 UNP G0S5R3 SEE REMARK 999 SEQADV 4GYI VAL A 22 UNP G0S5R3 SEE REMARK 999 SEQADV 4GYI GLU A 23 UNP G0S5R3 SEE REMARK 999 SEQRES 1 A 397 SER MET LYS LEU ASP THR ARG ALA MET ARG HIS LEU THR SEQRES 2 A 397 ALA GLU ASP TRP ARG VAL LEU THR ALA VAL GLU MET GLY SEQRES 3 A 397 SER LYS ASN HIS GLU ILE VAL PRO THR PRO LEU ILE GLU SEQRES 4 A 397 LYS ILE ALA ARG LEU ARG GLY GLY SER SER GLY VAL HIS SEQRES 5 A 397 LYS SER ILE ALA THR LEU ALA LYS ALA GLY LEU ILE ALA SEQRES 6 A 397 ARG MET LYS GLU ALA LYS TYR ASP GLY TYR ARG LEU THR SEQRES 7 A 397 TYR GLY GLY LEU ASP TYR LEU ALA LEU HIS THR HIS ALA SEQRES 8 A 397 ALA ARG LYS ASP VAL TYR SER VAL GLY SER ARG ILE GLY SEQRES 9 A 397 VAL GLY LYS GLU SER ASP ILE MET ILE VAL ALA ASP GLU SEQRES 10 A 397 LYS GLY LYS GLN LYS VAL LEU LYS ILE HIS ARG LEU GLY SEQRES 11 A 397 ARG ILE SER PHE ARG THR VAL LYS ALA ASN ARG ASP TYR SEQRES 12 A 397 LEU ARG ASN ARG SER THR GLY SER TRP MET TYR LEU SER SEQRES 13 A 397 ARG LEU ALA ALA ILE LYS GLU PHE ALA PHE MET LYS ALA SEQRES 14 A 397 LEU TYR GLU GLU GLY PHE PRO VAL PRO GLU PRO ILE ALA SEQRES 15 A 397 GLN SER ARG HIS THR ILE VAL MET SER LEU VAL ASP ALA SEQRES 16 A 397 LEU PRO MET ARG GLN VAL SER SER VAL PRO ASP PRO ALA SEQRES 17 A 397 SER LEU TYR ALA ASP LEU ILE ALA LEU ILE LEU ARG LEU SEQRES 18 A 397 ALA LYS HIS GLY LEU ILE HIS GLY ASP PHE ASN GLU PHE SEQRES 19 A 397 ASN ILE LEU ILE ARG GLU GLU LYS ASP ALA GLU ASP PRO SEQRES 20 A 397 SER SER ILE THR LEU THR PRO ILE ILE ILE PHD PHE PRO SEQRES 21 A 397 GLN MET VAL SER MET ASP HIS PRO ASN ALA GLU MET TYR SEQRES 22 A 397 PHE ASP ARG ASP VAL GLN CYS ILE LYS ARG PHE PHE GLU SEQRES 23 A 397 ARG ARG PHE HIS PHE VAL SER THR THR PRO GLY PRO PHE SEQRES 24 A 397 TYR LYS ASP ALA LYS LYS THR VAL GLY LYS ASP GLY ALA SEQRES 25 A 397 LYS ARG LEU ASP ALA ALA LEU GLU ALA SER GLY PHE THR SEQRES 26 A 397 LYS LYS MET ALA LYS ASP LEU GLU ALA ALA ILE ARG GLU SEQRES 27 A 397 GLN GLN GLU SER ARG ASN ASP GLU GLU ASP SER ASP ASP SEQRES 28 A 397 TYR GLU GLU ASP SER ASP LYS GLU LYS ALA SER ASN GLU SEQRES 29 A 397 ASP THR ASP VAL ASP ASP GLY ARG LEU GLN VAL ILE GLY SEQRES 30 A 397 ASP HIS VAL GLN LEU GLY THR GLU GLY ASP LEU LYS LYS SEQRES 31 A 397 LEU THR ILE ASN ASP GLY THR MODRES 4GYI PHD A 257 ASP ASPARTYL PHOSPHATE HET PHD A 257 12 HET ADP A 401 27 HET MG A 402 1 HET EDO A 403 4 HET EDO A 404 4 HETNAM PHD ASPARTYL PHOSPHATE HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 PHD C4 H8 N O7 P FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 MG MG 2+ FORMUL 4 EDO 2(C2 H6 O2) FORMUL 6 HOH *104(H2 O) HELIX 1 1 ARG A 6 HIS A 10 5 5 HELIX 2 2 THR A 12 SER A 26 1 15 HELIX 3 3 THR A 34 ARG A 42 1 9 HELIX 4 4 GLY A 49 ALA A 60 1 12 HELIX 5 5 THR A 77 ARG A 92 1 16 HELIX 6 6 SER A 147 GLU A 172 1 26 HELIX 7 7 ARG A 198 VAL A 200 5 3 HELIX 8 8 ASP A 205 HIS A 223 1 19 HELIX 9 9 ASN A 268 HIS A 289 1 22 HELIX 10 10 PHE A 298 LYS A 304 1 7 HELIX 11 11 ARG A 313 ALA A 317 5 5 HELIX 12 12 THR A 324 SER A 341 1 18 SHEET 1 A 3 VAL A 32 PRO A 33 0 SHEET 2 A 3 ASP A 72 LEU A 76 -1 O TYR A 74 N VAL A 32 SHEET 3 A 3 ILE A 63 LYS A 67 -1 N MET A 66 O GLY A 73 SHEET 1 B 5 SER A 97 VAL A 104 0 SHEET 2 B 5 SER A 108 ALA A 114 -1 O ILE A 112 N GLY A 99 SHEET 3 B 5 GLN A 120 HIS A 126 -1 O LYS A 121 N VAL A 113 SHEET 4 B 5 THR A 186 SER A 190 -1 O MET A 189 N VAL A 122 SHEET 5 B 5 PRO A 179 SER A 183 -1 N ALA A 181 O VAL A 188 SHEET 1 C 2 ARG A 130 ILE A 131 0 SHEET 2 C 2 ASP A 141 TYR A 142 -1 O ASP A 141 N ILE A 131 SHEET 1 D 3 LEU A 195 PRO A 196 0 SHEET 2 D 3 ILE A 235 LYS A 241 -1 O ILE A 237 N LEU A 195 SHEET 3 D 3 ILE A 249 ILE A 255 -1 O THR A 252 N ARG A 238 SHEET 1 E 2 LEU A 225 ILE A 226 0 SHEET 2 E 2 VAL A 262 SER A 263 -1 O VAL A 262 N ILE A 226 LINK C ILE A 256 N PHD A 257 1555 1555 1.33 LINK C PHD A 257 N PHE A 258 1555 1555 1.33 LINK OD1 ASN A 234 MG MG A 402 1555 1555 2.12 LINK OD1 PHD A 257 MG MG A 402 1555 1555 2.27 LINK O1A ADP A 401 MG MG A 402 1555 1555 2.03 LINK O2B ADP A 401 MG MG A 402 1555 1555 2.10 LINK MG MG A 402 O HOH A 523 1555 1555 2.08 LINK MG MG A 402 O HOH A 543 1555 1555 2.11 CISPEP 1 ARG A 44 GLY A 45 0 -1.63 CISPEP 2 GLY A 45 GLY A 46 0 0.87 CISPEP 3 SER A 47 SER A 48 0 -7.45 CISPEP 4 GLY A 296 PRO A 297 0 -0.19 CISPEP 5 VAL A 306 GLY A 307 0 -18.00 SITE 1 AC1 19 SER A 108 ILE A 110 LYS A 124 PRO A 177 SITE 2 AC1 19 MET A 189 SER A 190 VAL A 192 PRO A 196 SITE 3 AC1 19 PHE A 233 ASN A 234 ILE A 256 PHD A 257 SITE 4 AC1 19 MG A 402 HOH A 510 HOH A 523 HOH A 532 SITE 5 AC1 19 HOH A 543 HOH A 565 HOH A 566 SITE 1 AC2 5 ASN A 234 PHD A 257 ADP A 401 HOH A 523 SITE 2 AC2 5 HOH A 543 SITE 1 AC3 7 TYR A 78 HIS A 126 ARG A 127 LEU A 128 SITE 2 AC3 7 TYR A 142 SER A 155 HIS A 185 SITE 1 AC4 3 ARG A 156 GLN A 182 ARG A 184 CRYST1 119.624 119.624 71.783 90.00 90.00 120.00 H 3 9 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 0.008360 0.004826 0.000000 0.00000 SCALE2 0.000000 0.009653 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013931 0.00000