HEADER TRANSFERASE 17-JUN-15 5C3V OBSLTE 21-MAR-18 5C3V 6CMW TITLE AN ENZYME WITH BOUND LIGAND AND METAL COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHATIDYLINOSITOL-4-PHOSPHATE 5-KINASE, TYPE I, ALPHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 49-431; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: PIP5K1AA, PIP5K1A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KINASE, ATP, CALCIUM, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR X.K.ZENG,D.X.SUI,J.HU REVDAT 2 21-MAR-18 5C3V 1 OBSLTE REVDAT 1 21-DEC-16 5C3V 0 JRNL AUTH X.K.ZENG,D.X.SUI,J.HU JRNL TITL AN ENZYME WITH BOUND LIGAND AND METAL JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 10269 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1153 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 737 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE SET COUNT : 65 REMARK 3 BIN FREE R VALUE : 0.3330 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2364 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 87.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.41000 REMARK 3 B22 (A**2) : -0.41000 REMARK 3 B33 (A**2) : 0.82000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 1.273 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.392 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.282 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 35.084 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.922 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.895 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2462 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2229 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3333 ; 1.426 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5101 ; 0.781 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 304 ; 6.639 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 107 ;34.910 ;22.991 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 376 ;17.238 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;16.988 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 364 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2779 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 595 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1225 ; 2.603 ; 5.354 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1224 ; 2.602 ; 5.354 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1526 ; 4.183 ; 8.026 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 57 A 701 REMARK 3 ORIGIN FOR THE GROUP (A): -22.5366 14.7444 -19.9257 REMARK 3 T TENSOR REMARK 3 T11: 0.3495 T22: 0.1470 REMARK 3 T33: 0.0389 T12: 0.1590 REMARK 3 T13: 0.0979 T23: 0.0467 REMARK 3 L TENSOR REMARK 3 L11: 3.1132 L22: 4.6778 REMARK 3 L33: 3.3477 L12: 1.7341 REMARK 3 L13: -0.6132 L23: 0.2634 REMARK 3 S TENSOR REMARK 3 S11: 0.0776 S12: -0.3903 S13: 0.0957 REMARK 3 S21: 0.8587 S22: 0.0431 S23: 0.1623 REMARK 3 S31: 0.0352 S32: -0.0713 S33: -0.1207 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 5C3V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000210982. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0782 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11422 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.150 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 20.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 39.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG8000, 100 MM SODIUM CACODYLATE, REMARK 280 160 MM CA(AC)2, 20% GLYCEROL, PH 6.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 78.74200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 44.29500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 44.29500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 118.11300 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 44.29500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 44.29500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.37100 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 44.29500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.29500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 118.11300 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 44.29500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.29500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 39.37100 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 78.74200 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -78.74200 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 48 REMARK 465 THR A 49 REMARK 465 GLY A 50 REMARK 465 GLU A 51 REMARK 465 THR A 52 REMARK 465 THR A 53 REMARK 465 TYR A 54 REMARK 465 LYS A 55 REMARK 465 LYS A 56 REMARK 465 ARG A 311 REMARK 465 ALA A 312 REMARK 465 GLY A 313 REMARK 465 GLU A 314 REMARK 465 GLU A 315 REMARK 465 ALA A 316 REMARK 465 SER A 317 REMARK 465 THR A 318 REMARK 465 ALA A 319 REMARK 465 VAL A 320 REMARK 465 PRO A 321 REMARK 465 ASP A 322 REMARK 465 THR A 323 REMARK 465 GLN A 324 REMARK 465 LYS A 325 REMARK 465 LYS A 326 REMARK 465 GLY A 327 REMARK 465 GLN A 328 REMARK 465 GLY A 329 REMARK 465 GLN A 330 REMARK 465 LYS A 331 REMARK 465 PRO A 332 REMARK 465 LEU A 333 REMARK 465 TYR A 334 REMARK 465 CYS A 335 REMARK 465 THR A 336 REMARK 465 ALA A 337 REMARK 465 ILE A 338 REMARK 465 GLU A 339 REMARK 465 SER A 340 REMARK 465 ILE A 341 REMARK 465 GLN A 342 REMARK 465 GLY A 343 REMARK 465 GLU A 344 REMARK 465 SER A 345 REMARK 465 LYS A 346 REMARK 465 SER A 347 REMARK 465 LYS A 348 REMARK 465 THR A 349 REMARK 465 SER A 350 REMARK 465 PRO A 351 REMARK 465 GLN A 352 REMARK 465 PRO A 353 REMARK 465 TYR A 354 REMARK 465 GLU A 355 REMARK 465 SER A 356 REMARK 465 LEU A 385 REMARK 465 VAL A 386 REMARK 465 LYS A 387 REMARK 465 LYS A 388 REMARK 465 LEU A 389 REMARK 465 GLU A 390 REMARK 465 HIS A 391 REMARK 465 SER A 392 REMARK 465 TRP A 393 REMARK 465 LYS A 394 REMARK 465 ALA A 395 REMARK 465 LEU A 396 REMARK 465 LEU A 397 REMARK 465 HIS A 398 REMARK 465 ASP A 399 REMARK 465 GLY A 400 REMARK 465 ASP A 401 REMARK 465 SER A 427 REMARK 465 GLN A 428 REMARK 465 LEU A 429 REMARK 465 LYS A 430 REMARK 465 THR A 431 REMARK 465 LEU A 432 REMARK 465 GLU A 433 REMARK 465 HIS A 434 REMARK 465 HIS A 435 REMARK 465 HIS A 436 REMARK 465 HIS A 437 REMARK 465 HIS A 438 REMARK 465 HIS A 439 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 57 OG1 CG2 REMARK 470 LYS A 80 CG CD CE NZ REMARK 470 SER A 100 OG REMARK 470 GLN A 101 CG CD OE1 NE2 REMARK 470 SER A 103 OG REMARK 470 SER A 104 OG REMARK 470 SER A 105 OG REMARK 470 LYS A 115 CG CD CE NZ REMARK 470 SER A 151 OG REMARK 470 SER A 156 OG REMARK 470 ASP A 212 CG OD1 OD2 REMARK 470 LYS A 214 CG CD CE NZ REMARK 470 ILE A 216 CG1 CG2 CD1 REMARK 470 VAL A 229 CG1 CG2 REMARK 470 LYS A 243 CG CD CE NZ REMARK 470 ARG A 245 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 253 CG CD CE NZ REMARK 470 GLU A 269 CG CD OE1 OE2 REMARK 470 ASN A 275 CG OD1 ND2 REMARK 470 ASP A 276 CG OD1 OD2 REMARK 470 SER A 282 OG REMARK 470 MET A 357 CG SD CE REMARK 470 PHE A 363 CG CD1 CD2 CE1 CE2 CZ REMARK 470 SER A 365 OG REMARK 470 LYS A 366 CG CD CE NZ REMARK 470 ARG A 369 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 371 CG CD1 CD2 REMARK 470 VAL A 372 CG1 CG2 REMARK 470 GLN A 381 CG CD OE1 NE2 REMARK 470 ARG A 384 CG CD NE CZ NH1 NH2 REMARK 470 THR A 402 OG1 CG2 REMARK 470 VAL A 403 CG1 CG2 REMARK 470 SER A 404 OG REMARK 470 VAL A 405 CG1 CG2 REMARK 470 LYS A 417 CG CD CE NZ REMARK 470 LYS A 426 CG CD CE NZ 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 ARG A 125 NE - CZ - NH1 ANGL. DEV. = 3.2 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 146 128.16 -39.09 REMARK 500 SER A 151 92.15 -62.63 REMARK 500 ASN A 152 -144.38 62.67 REMARK 500 ASP A 212 65.19 13.67 REMARK 500 LYS A 243 46.62 35.75 REMARK 500 ARG A 244 46.69 -96.48 REMARK 500 PHE A 363 -168.51 -121.84 REMARK 500 SER A 365 99.20 -44.41 REMARK 500 ASP A 378 61.42 71.69 REMARK 500 SER A 421 -35.47 -132.76 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 A 503 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 378 OD1 REMARK 620 2 ASP A 378 OD2 55.9 REMARK 620 3 ATP A 501 O1G 112.4 65.1 REMARK 620 4 ATP A 501 O1B 82.3 81.9 58.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 502 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 378 OD2 REMARK 620 2 ATP A 501 O2G 100.3 REMARK 620 3 ATP A 501 O2A 80.5 80.8 REMARK 620 N 1 2 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 503 DBREF 5C3V A 49 431 UNP Q503I3 Q503I3_DANRE 49 431 SEQADV 5C3V MET A 48 UNP Q503I3 INITIATING METHIONINE SEQADV 5C3V LEU A 432 UNP Q503I3 EXPRESSION TAG SEQADV 5C3V GLU A 433 UNP Q503I3 EXPRESSION TAG SEQADV 5C3V HIS A 434 UNP Q503I3 EXPRESSION TAG SEQADV 5C3V HIS A 435 UNP Q503I3 EXPRESSION TAG SEQADV 5C3V HIS A 436 UNP Q503I3 EXPRESSION TAG SEQADV 5C3V HIS A 437 UNP Q503I3 EXPRESSION TAG SEQADV 5C3V HIS A 438 UNP Q503I3 EXPRESSION TAG SEQADV 5C3V HIS A 439 UNP Q503I3 EXPRESSION TAG SEQRES 1 A 392 MET THR GLY GLU THR THR TYR LYS LYS THR THR SER SER SEQRES 2 A 392 ALA LEU LYS GLY ALA ILE GLN LEU GLY ILE THR HIS SER SEQRES 3 A 392 VAL GLY SER LEU SER GLN LYS PRO GLU ARG ASP VAL LEU SEQRES 4 A 392 MET GLN ASP PHE GLU VAL VAL GLU SER ILE PHE PHE PRO SEQRES 5 A 392 SER GLN GLY SER SER SER THR PRO GLY HIS HIS HIS GLY SEQRES 6 A 392 ASP PHE LYS PHE LYS THR TYR ALA PRO ILE ALA PHE ARG SEQRES 7 A 392 TYR PHE ARG GLU MET PHE GLY ILE ARG PRO ASP ASP TYR SEQRES 8 A 392 LEU TYR SER LEU CYS ASN GLU PRO LEU ILE GLU LEU SER SEQRES 9 A 392 ASN PRO GLY ALA SER GLY SER LEU PHE TYR VAL SER SER SEQRES 10 A 392 ASP ASP GLU PHE ILE ILE LYS THR VAL GLN HIS LYS GLU SEQRES 11 A 392 ALA GLU PHE LEU GLN THR LEU LEU PRO GLY TYR PHE MET SEQRES 12 A 392 ASN LEU ASN GLN ASN MET ARG THR LEU LEU PRO LYS PHE SEQRES 13 A 392 TYR GLY LEU TYR CYS VAL GLN ALA ASP GLY LYS ASN ILE SEQRES 14 A 392 ARG ILE VAL VAL MET ASN ASN LEU LEU PRO ARG ALA VAL SEQRES 15 A 392 PRO MET HIS LEU LYS PHE ASP LEU LYS GLY SER THR TYR SEQRES 16 A 392 LYS ARG ARG ALA SER PRO LYS GLU ARG SER LYS GLY VAL SEQRES 17 A 392 PRO THR TYR LYS ASP LEU ASP PHE MET GLN ASP MET PRO SEQRES 18 A 392 GLU GLY ILE LEU LEU GLU ASN ASP HIS TYR THR ALA LEU SEQRES 19 A 392 SER ARG THR MET GLN ARG ASP CYS ARG VAL LEU GLN SER SEQRES 20 A 392 PHE LYS ILE MET ASP TYR SER LEU LEU VAL GLY ILE HIS SEQRES 21 A 392 ILE LEU HIS ARG ALA GLY GLU GLU ALA SER THR ALA VAL SEQRES 22 A 392 PRO ASP THR GLN LYS LYS GLY GLN GLY GLN LYS PRO LEU SEQRES 23 A 392 TYR CYS THR ALA ILE GLU SER ILE GLN GLY GLU SER LYS SEQRES 24 A 392 SER LYS THR SER PRO GLN PRO TYR GLU SER MET GLY GLY SEQRES 25 A 392 ILE PRO ALA PHE ASN SER LYS GLY GLU ARG LEU LEU VAL SEQRES 26 A 392 PHE ILE GLY ILE ILE ASP ILE LEU GLN SER TYR ARG LEU SEQRES 27 A 392 VAL LYS LYS LEU GLU HIS SER TRP LYS ALA LEU LEU HIS SEQRES 28 A 392 ASP GLY ASP THR VAL SER VAL HIS ARG PRO SER PHE TYR SEQRES 29 A 392 ALA ASP ARG PHE GLN LYS PHE MET CYS SER THR VAL PHE SEQRES 30 A 392 ARG LYS SER GLN LEU LYS THR LEU GLU HIS HIS HIS HIS SEQRES 31 A 392 HIS HIS HET ATP A 501 31 HET CA A 502 1 HET CA A 503 1 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM CA CALCIUM ION FORMUL 2 ATP C10 H16 N5 O13 P3 FORMUL 3 CA 2(CA 2+) HELIX 1 AA1 THR A 57 SER A 78 1 22 HELIX 2 AA2 LEU A 86 GLU A 91 1 6 HELIX 3 AA3 ALA A 120 PHE A 131 1 12 HELIX 4 AA4 ARG A 134 ASN A 144 1 11 HELIX 5 AA5 GLN A 174 ASN A 193 1 20 HELIX 6 AA6 SER A 247 SER A 252 1 6 HELIX 7 AA7 ASP A 260 MET A 267 1 8 HELIX 8 AA8 GLU A 274 PHE A 295 1 22 HELIX 9 AA9 HIS A 406 CYS A 420 1 15 SHEET 1 AA1 7 VAL A 93 PHE A 98 0 SHEET 2 AA1 7 PHE A 114 TYR A 119 -1 O THR A 118 N GLU A 94 SHEET 3 AA1 7 GLY A 205 ALA A 211 -1 O LEU A 206 N TYR A 119 SHEET 4 AA1 7 LYS A 214 ASN A 222 -1 O ILE A 216 N VAL A 209 SHEET 5 AA1 7 PHE A 168 VAL A 173 -1 N ILE A 169 O MET A 221 SHEET 6 AA1 7 PHE A 160 VAL A 162 -1 N TYR A 161 O ILE A 170 SHEET 7 AA1 7 ILE A 148 LEU A 150 -1 N ILE A 148 O VAL A 162 SHEET 1 AA2 5 THR A 257 LYS A 259 0 SHEET 2 AA2 5 LEU A 233 LEU A 237 1 N ASP A 236 O TYR A 258 SHEET 3 AA2 5 SER A 301 ILE A 308 -1 O VAL A 304 N PHE A 235 SHEET 4 AA2 5 LEU A 370 ILE A 377 -1 O PHE A 373 N GLY A 305 SHEET 5 AA2 5 ILE A 360 ALA A 362 -1 N ALA A 362 O LEU A 370 LINK OD1 ASP A 378 CA CA A 503 1555 1555 2.34 LINK OD2 ASP A 378 CA CA A 502 1555 1555 2.33 LINK OD2 ASP A 378 CA CA A 503 1555 1555 2.34 LINK O1G ATP A 501 CA CA A 503 1555 1555 2.32 LINK O2G ATP A 501 CA CA A 502 1555 1555 2.34 LINK O1B ATP A 501 CA CA A 503 1555 1555 2.34 LINK O2A ATP A 501 CA CA A 502 1555 1555 2.30 CISPEP 1 ASN A 152 PRO A 153 0 -7.06 SITE 1 AC1 16 GLY A 154 ALA A 155 SER A 156 SER A 158 SITE 2 AC1 16 PHE A 160 ILE A 169 LYS A 171 ASN A 222 SITE 3 AC1 16 ASN A 223 LEU A 224 ASP A 236 THR A 257 SITE 4 AC1 16 LEU A 303 ASP A 378 CA A 502 CA A 503 SITE 1 AC2 2 ASP A 378 ATP A 501 SITE 1 AC3 2 ASP A 378 ATP A 501 CRYST1 88.590 88.590 157.484 90.00 90.00 90.00 P 43 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.011288 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011288 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006350 0.00000