PDB Short entry for 5I0N HEADER TRANSFERASE 04-FEB-16 5I0N TITLE PI4K IIALPHA BOUND TO CALCIUM CAVEAT 5I0N RESIDUE A LYS 172 AND RESIDUE A GLY 1001 ARE NOT PROPERLY CAVEAT 2 5I0N LINKED: DISTANCE BETWEEN C AND N IS 4.16. RESIDUE A LEU CAVEAT 3 5I0N 1166 AND RESIDUE A GLY 180 ARE NOT PROPERLY LINKED: CAVEAT 4 5I0N DISTANCE BETWEEN C AND N IS 3.51. RESIDUE A ILE 304 AND CAVEAT 5 5I0N RESIDUE A ARG 305 ARE NOT PROPERLY LINKED: DISTANCE BETWEEN CAVEAT 6 5I0N C AND N IS 1.10. RESIDUE A ARG 305 AND RESIDUE A ASN 306 CAVEAT 7 5I0N ARE NOT PROPERLY LINKED: DISTANCE BETWEEN C AND N IS 1.19. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHATIDYLINOSITOL 4-KINASE TYPE 2-ALPHA,LYSOZYME, COMPND 3 PHOSPHATIDYLINOSITOL 4-KINASE TYPE 2-ALPHA; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: PHOSPHATIDYLINOSITOL 4-KINASE TYPE II-ALPHA, COMPND 6 PHOSPHATIDYLINOSITOL 4-KINASE TYPE II-ALPHA; COMPND 7 EC: 2.7.1.67,3.2.1.17,2.7.1.67; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS, ENTEROBACTERIA PHAGE T4; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606, 10665; SOURCE 5 GENE: PI4K2A, E, T4TP126; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KINASE, CALCIUM, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.BAUMLOVA,E.BOURA REVDAT 3 10-JAN-24 5I0N 1 LINK REVDAT 2 06-SEP-17 5I0N 1 REMARK REVDAT 1 09-MAR-16 5I0N 0 JRNL AUTH A.BAUMLOVA,E.BOURA JRNL TITL PI4K IIALPHA BOUND TO CALCIUM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 29698 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1507 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 48.9642 - 5.0691 1.00 2744 137 0.1830 0.2019 REMARK 3 2 5.0691 - 4.0241 1.00 2611 127 0.1755 0.2152 REMARK 3 3 4.0241 - 3.5156 1.00 2573 144 0.1986 0.2336 REMARK 3 4 3.5156 - 3.1942 1.00 2573 138 0.2277 0.2689 REMARK 3 5 3.1942 - 2.9653 1.00 2538 144 0.2576 0.2858 REMARK 3 6 2.9653 - 2.7905 1.00 2540 142 0.2627 0.3145 REMARK 3 7 2.7905 - 2.6507 1.00 2527 128 0.2600 0.3511 REMARK 3 8 2.6507 - 2.5354 1.00 2521 141 0.2674 0.3253 REMARK 3 9 2.5354 - 2.4378 1.00 2524 138 0.2861 0.3414 REMARK 3 10 2.4378 - 2.3536 1.00 2516 139 0.3141 0.3774 REMARK 3 11 2.3536 - 2.2801 1.00 2524 129 0.3362 0.3850 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.460 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.009 4099 REMARK 3 ANGLE : 0.992 5568 REMARK 3 CHIRALITY : 0.037 601 REMARK 3 PLANARITY : 0.003 708 REMARK 3 DIHEDRAL : 19.433 2502 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5I0N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1000218056. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-AUG-15 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 : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9834 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29715 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.280 REMARK 200 RESOLUTION RANGE LOW (A) : 48.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.13200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.1600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 1.37000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.460 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4PLA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12.5% W/V PEG 1000, 12.5% W/V PEG REMARK 280 3350, 12.5% V/V MPD, 0.1 M BICINE/TRIZMA BASE PH 8.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+1/2,Y+1/2,-Z REMARK 290 4555 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 39.44100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.01400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.44100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.01400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 TOTAL BURIED SURFACE AREA: 1580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 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 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 72 REMARK 465 ALA A 73 REMARK 465 MET A 74 REMARK 465 GLY A 75 REMARK 465 THR A 76 REMARK 465 VAL A 77 REMARK 465 ALA A 78 REMARK 465 ALA A 79 REMARK 465 GLN A 80 REMARK 465 ALA A 81 REMARK 465 GLN A 82 REMARK 465 ALA A 83 REMARK 465 LEU A 84 REMARK 465 ALA A 85 REMARK 465 ALA A 86 REMARK 465 GLN A 87 REMARK 465 ALA A 88 REMARK 465 ALA A 89 REMARK 465 ALA A 90 REMARK 465 ALA A 91 REMARK 465 ALA A 92 REMARK 465 HIS A 93 REMARK 465 ALA A 94 REMARK 465 ALA A 95 REMARK 465 GLN A 96 REMARK 465 ALA A 97 REMARK 465 HIS A 98 REMARK 465 ARG A 99 REMARK 465 GLY A 133 REMARK 465 SER A 134 REMARK 465 LEU A 236 REMARK 465 ALA A 237 REMARK 465 LEU A 238 REMARK 465 GLU A 239 REMARK 465 LYS A 240 REMARK 465 VAL A 241 REMARK 465 PRO A 242 REMARK 465 LYS A 243 REMARK 465 VAL A 244 REMARK 465 GLY A 245 REMARK 465 GLN A 246 REMARK 465 ARG A 247 REMARK 465 PHE A 248 REMARK 465 PRO A 321 REMARK 465 MET A 322 REMARK 465 ASP A 323 REMARK 465 SER A 324 REMARK 465 SER A 325 REMARK 465 SER A 326 REMARK 465 SER A 327 REMARK 465 ARG A 328 REMARK 465 ASP A 329 REMARK 465 THR A 330 REMARK 465 ARG A 455 REMARK 465 SER A 456 REMARK 465 HIS A 457 REMARK 465 GLN A 458 REMARK 465 ARG A 459 REMARK 465 SER A 460 REMARK 465 SER A 461 REMARK 465 SER A 462 REMARK 465 GLU A 463 REMARK 465 SER A 464 REMARK 465 TYR A 465 REMARK 465 THR A 466 REMARK 465 GLN A 467 REMARK 465 SER A 468 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 GLU A 100 CG CD OE1 OE2 REMARK 470 ARG A 101 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 132 CG CD OE1 NE2 REMARK 470 LYS A 165 CG CD CE NZ REMARK 470 ARG A1139 CG CD NE CZ NH1 NH2 REMARK 470 LEU A1166 CG CD1 CD2 REMARK 470 ARG A 181 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 235 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 249 CG OD1 ND2 REMARK 470 ASP A 331 CG OD1 OD2 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 O HOH A 1485 O HOH A 1519 1.43 REMARK 500 N GLY A 425 O HOH A 1301 1.81 REMARK 500 NH2 ARG A 288 O HOH A 1302 1.82 REMARK 500 OD2 ASP A 200 O HOH A 1303 1.83 REMARK 500 OE2 GLU A 1047 O HOH A 1304 1.83 REMARK 500 O HOH A 1344 O HOH A 1468 1.84 REMARK 500 O LYS A 1137 O HOH A 1305 1.86 REMARK 500 OE2 GLU A 193 O HOH A 1306 1.87 REMARK 500 O GLN A 132 O HOH A 1307 1.88 REMARK 500 CG ASP A 200 O HOH A 1303 1.89 REMARK 500 NZ LYS A 1021 O HOH A 1308 1.91 REMARK 500 OE1 GLU A 193 O HOH A 1306 1.92 REMARK 500 OD1 ASP A 271 O HOH A 1309 1.92 REMARK 500 O VAL A 185 O HOH A 1310 1.93 REMARK 500 NH1 ARG A 123 O HOH A 1311 1.94 REMARK 500 O HOH A 1420 O HOH A 1492 1.94 REMARK 500 SG CYS A 183 O HOH A 1326 1.94 REMARK 500 N ASN A 347 O HOH A 1306 1.95 REMARK 500 OE1 GLU A 103 O HOH A 1312 1.97 REMARK 500 O ARG A 101 O HOH A 1313 1.99 REMARK 500 O VAL A 422 O HOH A 1301 1.99 REMARK 500 O HOH A 1438 O HOH A 1494 1.99 REMARK 500 OD1 ASP A 200 O HOH A 1303 2.00 REMARK 500 O ALA A 421 O HOH A 1301 2.01 REMARK 500 C GLN A 132 O HOH A 1307 2.01 REMARK 500 N ASP A 1091 O HOH A 1314 2.04 REMARK 500 CA ASP A 346 O HOH A 1306 2.07 REMARK 500 CD GLU A 1047 O HOH A 1304 2.08 REMARK 500 OD2 ASP A 227 O HOH A 1315 2.08 REMARK 500 NH2 ARG A 1156 O HOH A 1316 2.12 REMARK 500 NH2 ARG A 276 O HOH A 1317 2.12 REMARK 500 CD GLU A 193 O HOH A 1306 2.14 REMARK 500 O1G ATP A 1202 O HOH A 1318 2.14 REMARK 500 ND1 HIS A 355 O HOH A 1319 2.14 REMARK 500 OE1 GLU A 1130 O HOH A 1320 2.17 REMARK 500 N ASN A 102 O HOH A 1321 2.19 REMARK 500 O MET A 446 O HOH A 1322 2.19 REMARK 500 N ASN A 187 O HOH A 1323 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 O HOH A 1428 O HOH A 1455 4555 2.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ILE A 304 C ARG A 305 N -0.240 REMARK 500 ARG A 305 C ASN A 306 N -0.148 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 GLY A1158 CA - C - N ANGL. DEV. = 17.8 DEGREES REMARK 500 GLY A1158 O - C - N ANGL. DEV. = -18.6 DEGREES REMARK 500 THR A1159 C - N - CA ANGL. DEV. = 20.8 DEGREES REMARK 500 ARG A 305 C - N - CA ANGL. DEV. = 17.0 DEGREES REMARK 500 ASP A 319 CA - C - N ANGL. DEV. = 15.0 DEGREES REMARK 500 ASP A 319 O - C - N ANGL. DEV. = -15.5 DEGREES REMARK 500 CYS A 320 C - N - CA ANGL. DEV. = 16.9 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 ASN A 102 66.95 -67.78 REMARK 500 ILE A1031 75.63 -101.54 REMARK 500 ARG A 305 62.67 69.21 REMARK 500 ASP A 319 45.32 -93.92 REMARK 500 ASN A 347 41.70 -103.16 REMARK 500 LYS A 387 -60.07 -95.06 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 CA A1203 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 313 OD1 REMARK 620 2 ASP A 346 OD2 73.7 REMARK 620 3 ATP A1201 O2G 134.9 70.5 REMARK 620 4 ATP A1201 O3G 163.0 120.2 52.3 REMARK 620 5 ATP A1201 O1A 117.8 76.2 79.0 77.2 REMARK 620 6 HOH A1340 O 83.0 125.8 96.3 80.6 155.0 REMARK 620 7 HOH A1386 O 84.8 130.4 139.9 91.7 75.5 94.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1204 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 346 OD1 REMARK 620 2 ASP A 346 OD2 52.0 REMARK 620 3 ATP A1201 O2G 114.4 67.8 REMARK 620 4 ATP A1201 O2B 83.0 81.4 63.2 REMARK 620 5 HOH A1354 O 79.2 83.7 120.3 161.5 REMARK 620 6 HOH A1478 O 155.5 146.8 79.1 85.7 112.7 REMARK 620 7 HOH A1504 O 106.2 158.1 132.4 99.6 90.2 54.5 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 ATP A 1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ATP A 1202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 1203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 1204 DBREF 5I0N A 76 172 UNP Q9BTU6 P4K2A_HUMAN 76 172 DBREF 5I0N A 1004 1166 UNP D9IEF7 D9IEF7_BPT4 2 164 DBREF 5I0N A 180 468 UNP Q9BTU6 P4K2A_HUMAN 180 468 SEQADV 5I0N GLY A 72 UNP Q9BTU6 EXPRESSION TAG SEQADV 5I0N ALA A 73 UNP Q9BTU6 EXPRESSION TAG SEQADV 5I0N MET A 74 UNP Q9BTU6 EXPRESSION TAG SEQADV 5I0N GLY A 75 UNP Q9BTU6 EXPRESSION TAG SEQADV 5I0N GLY A 1001 UNP Q9BTU6 LINKER SEQADV 5I0N THR A 1002 UNP Q9BTU6 LINKER SEQADV 5I0N GLY A 1003 UNP Q9BTU6 LINKER SEQADV 5I0N THR A 1056 UNP D9IEF7 CYS 54 CONFLICT SEQADV 5I0N ALA A 1099 UNP D9IEF7 CYS 97 CONFLICT SEQRES 1 A 556 GLY ALA MET GLY THR VAL ALA ALA GLN ALA GLN ALA LEU SEQRES 2 A 556 ALA ALA GLN ALA ALA ALA ALA ALA HIS ALA ALA GLN ALA SEQRES 3 A 556 HIS ARG GLU ARG ASN GLU PHE PRO GLU ASP PRO GLU PHE SEQRES 4 A 556 GLU ALA VAL VAL ARG GLN ALA GLU LEU ALA ILE GLU ARG SEQRES 5 A 556 CYS ILE PHE PRO GLU ARG ILE TYR GLN GLY SER SER GLY SEQRES 6 A 556 SER TYR PHE VAL LYS ASP PRO GLN GLY ARG ILE ILE ALA SEQRES 7 A 556 VAL PHE LYS PRO LYS ASN GLU GLU PRO TYR GLY HIS LEU SEQRES 8 A 556 ASN PRO LYS TRP THR LYS TRP LEU GLN LYS GLY THR GLY SEQRES 9 A 556 ASN ILE PHE GLU MET LEU ARG ILE ASP GLU GLY LEU ARG SEQRES 10 A 556 LEU LYS ILE TYR LYS ASP THR GLU GLY TYR TYR THR ILE SEQRES 11 A 556 GLY ILE GLY HIS LEU LEU THR LYS SER PRO SER LEU ASN SEQRES 12 A 556 ALA ALA LYS SER GLU LEU ASP LYS ALA ILE GLY ARG ASN SEQRES 13 A 556 THR ASN GLY VAL ILE THR LYS ASP GLU ALA GLU LYS LEU SEQRES 14 A 556 PHE ASN GLN ASP VAL ASP ALA ALA VAL ARG GLY ILE LEU SEQRES 15 A 556 ARG ASN ALA LYS LEU LYS PRO VAL TYR ASP SER LEU ASP SEQRES 16 A 556 ALA VAL ARG ARG ALA ALA LEU ILE ASN MET VAL PHE GLN SEQRES 17 A 556 MET GLY GLU THR GLY VAL ALA GLY PHE THR ASN SER LEU SEQRES 18 A 556 ARG MET LEU GLN GLN LYS ARG TRP ASP GLU ALA ALA VAL SEQRES 19 A 556 ASN LEU ALA LYS SER ARG TRP TYR ASN GLN THR PRO ASN SEQRES 20 A 556 ARG ALA LYS ARG VAL ILE THR THR PHE ARG THR GLY THR SEQRES 21 A 556 TRP ASP ALA TYR LYS ASN LEU GLY ARG ASP CYS LEU VAL SEQRES 22 A 556 LEU ASN GLN GLY TYR LEU SER GLU ALA GLY ALA SER LEU SEQRES 23 A 556 VAL ASP GLN LYS LEU GLU LEU ASN ILE VAL PRO ARG THR SEQRES 24 A 556 LYS VAL VAL TYR LEU ALA SER GLU THR PHE ASN TYR SER SEQRES 25 A 556 ALA ILE ASP ARG VAL LYS SER ARG GLY LYS ARG LEU ALA SEQRES 26 A 556 LEU GLU LYS VAL PRO LYS VAL GLY GLN ARG PHE ASN ARG SEQRES 27 A 556 ILE GLY LEU PRO PRO LYS VAL GLY SER PHE GLN LEU PHE SEQRES 28 A 556 VAL GLU GLY TYR LYS ASP ALA ASP TYR TRP LEU ARG ARG SEQRES 29 A 556 PHE GLU ALA GLU PRO LEU PRO GLU ASN THR ASN ARG GLN SEQRES 30 A 556 LEU LEU LEU GLN PHE GLU ARG LEU VAL VAL LEU ASP TYR SEQRES 31 A 556 ILE ILE ARG ASN THR ASP ARG GLY ASN ASP ASN TRP LEU SEQRES 32 A 556 ILE LYS TYR ASP CYS PRO MET ASP SER SER SER SER ARG SEQRES 33 A 556 ASP THR ASP TRP VAL VAL VAL LYS GLU PRO VAL ILE LYS SEQRES 34 A 556 VAL ALA ALA ILE ASP ASN GLY LEU ALA PHE PRO LEU LYS SEQRES 35 A 556 HIS PRO ASP SER TRP ARG ALA TYR PRO PHE TYR TRP ALA SEQRES 36 A 556 TRP LEU PRO GLN ALA LYS VAL PRO PHE SER GLN GLU ILE SEQRES 37 A 556 LYS ASP LEU ILE LEU PRO LYS ILE SER ASP PRO ASN PHE SEQRES 38 A 556 VAL LYS ASP LEU GLU GLU ASP LEU TYR GLU LEU PHE LYS SEQRES 39 A 556 LYS ASP PRO GLY PHE ASP ARG GLY GLN PHE HIS LYS GLN SEQRES 40 A 556 ILE ALA VAL MET ARG GLY GLN ILE LEU ASN LEU THR GLN SEQRES 41 A 556 ALA LEU LYS ASP ASN LYS SER PRO LEU HIS LEU VAL GLN SEQRES 42 A 556 MET PRO PRO VAL ILE VAL GLU THR ALA ARG SER HIS GLN SEQRES 43 A 556 ARG SER SER SER GLU SER TYR THR GLN SER HET ATP A1201 43 HET ATP A1202 43 HET CA A1203 1 HET CA A1204 1 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM CA CALCIUM ION FORMUL 2 ATP 2(C10 H16 N5 O13 P3) FORMUL 4 CA 2(CA 2+) FORMUL 6 HOH *222(H2 O) HELIX 1 AA1 ASP A 107 ARG A 123 1 17 HELIX 2 AA2 ASN A 155 GLU A 157 5 3 HELIX 3 AA3 TRP A 166 LYS A 172 1 7 HELIX 4 AA4 GLY A 1001 GLY A 1003 5 3 HELIX 5 AA5 ASN A 1004 GLY A 1014 1 11 HELIX 6 AA6 SER A 1040 GLY A 1053 1 14 HELIX 7 AA7 THR A 1061 ASN A 1083 1 23 HELIX 8 AA8 LYS A 1085 SER A 1092 1 8 HELIX 9 AA9 ASP A 1094 GLY A 1115 1 22 HELIX 10 AB1 PHE A 1116 GLN A 1125 1 10 HELIX 11 AB2 ARG A 1127 ALA A 1136 1 10 HELIX 12 AB3 SER A 1138 THR A 1144 1 7 HELIX 13 AB4 THR A 1144 GLY A 1158 1 15 HELIX 14 AB5 TRP A 1160 LYS A 1164 5 5 HELIX 15 AB6 GLN A 188 GLU A 204 1 17 HELIX 16 AB7 SER A 224 ARG A 232 1 9 HELIX 17 AB8 ALA A 270 GLU A 280 1 11 HELIX 18 AB9 PRO A 283 ARG A 305 1 23 HELIX 19 AC1 PHE A 364 VAL A 374 5 11 HELIX 20 AC2 SER A 377 SER A 389 1 13 HELIX 21 AC3 ASP A 390 LYS A 406 1 17 HELIX 22 AC4 ASP A 412 ASP A 436 1 25 HELIX 23 AC5 SER A 439 GLN A 445 1 7 SHEET 1 AA1 5 GLU A 128 ARG A 129 0 SHEET 2 AA1 5 TYR A 138 LYS A 141 -1 O PHE A 139 N GLU A 128 SHEET 3 AA1 5 ILE A 147 PRO A 153 -1 O ILE A 148 N VAL A 140 SHEET 4 AA1 5 LYS A 256 LEU A 262 -1 O GLN A 261 N VAL A 150 SHEET 5 AA1 5 THR A 211 LEU A 216 -1 N VAL A 214 O GLY A 258 SHEET 1 AA2 3 ARG A1016 LYS A1021 0 SHEET 2 AA2 3 TYR A1027 GLY A1030 -1 O THR A1028 N TYR A1020 SHEET 3 AA2 3 HIS A1033 THR A1036 -1 O LEU A1035 N TYR A1027 SHEET 1 AA3 3 LYS A 268 ASP A 269 0 SHEET 2 AA3 3 TRP A 314 TYR A 318 -1 O ILE A 316 N LYS A 268 SHEET 3 AA3 3 ILE A 340 ALA A 344 -1 O ALA A 343 N LEU A 315 LINK OD1 ASN A 313 CA CA A1203 1555 1555 2.62 LINK OD2 ASP A 346 CA CA A1203 1555 1555 2.33 LINK OD1 ASP A 346 CA CA A1204 1555 1555 2.61 LINK OD2 ASP A 346 CA CA A1204 1555 1555 2.36 LINK O2G ATP A1201 CA CA A1203 1555 1555 2.32 LINK O3G ATP A1201 CA CA A1203 1555 1555 3.02 LINK O1A ATP A1201 CA CA A1203 1555 1555 2.43 LINK O2G ATP A1201 CA CA A1204 1555 1555 2.46 LINK O2B ATP A1201 CA CA A1204 1555 1555 2.41 LINK CA CA A1203 O HOH A1340 1555 1555 2.57 LINK CA CA A1203 O HOH A1386 1555 1555 2.63 LINK CA CA A1204 O HOH A1354 1555 1555 2.22 LINK CA CA A1204 O HOH A1478 1555 1555 2.63 LINK CA CA A1204 O HOH A1504 1555 1555 2.17 SITE 1 AC1 19 GLN A 132 SER A 137 PHE A 139 VAL A 150 SITE 2 AC1 19 LYS A 152 PRO A 209 LYS A 234 GLN A 261 SITE 3 AC1 19 LEU A 262 PHE A 263 VAL A 264 ILE A 345 SITE 4 AC1 19 ASP A 346 CA A1203 CA A1204 HOH A1307 SITE 5 AC1 19 HOH A1418 HOH A1428 HOH A1467 SITE 1 AC2 14 TRP A 359 ARG A 360 PRO A 363 PHE A 364 SITE 2 AC2 14 ALA A 367 TRP A 368 VAL A 444 GLN A 445 SITE 3 AC2 14 HOH A1318 HOH A1341 HOH A1342 HOH A1357 SITE 4 AC2 14 HOH A1375 HOH A1399 SITE 1 AC3 5 ASN A 313 ASP A 346 ATP A1201 HOH A1340 SITE 2 AC3 5 HOH A1386 SITE 1 AC4 5 ASP A 346 ATP A1201 HOH A1354 HOH A1478 SITE 2 AC4 5 HOH A1504 CRYST1 78.882 102.028 78.929 90.00 90.00 90.00 P 21 21 2 4 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 0.012677 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009801 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012670 0.00000