HEADER TRANSFERASE 04-OCT-15 5E3U TITLE CRYSTAL STRUCTURE OF PHOSPHATIDYLINOSITOL-4-PHOSPHATE 5-KINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHATIDYLINOSITOL-4-PHOSPHATE 5-KINASE, TYPE I, ALPHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 56-427; COMPND 5 SYNONYM: UNCHARACTERIZED PROTEIN; COMPND 6 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, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.MUFTUOGLU REVDAT 4 06-MAR-24 5E3U 1 JRNL REMARK REVDAT 3 10-AUG-16 5E3U 1 JRNL REVDAT 2 03-AUG-16 5E3U 1 JRNL REVDAT 1 20-JUL-16 5E3U 0 JRNL AUTH Y.MUFTUOGLU,Y.XUE,X.GAO,D.WU,Y.HA JRNL TITL MECHANISM OF SUBSTRATE SPECIFICITY OF PHOSPHATIDYLINOSITOL JRNL TITL 2 PHOSPHATE KINASES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 113 8711 2016 JRNL REFN ESSN 1091-6490 JRNL PMID 27439870 JRNL DOI 10.1073/PNAS.1522112113 REMARK 2 REMARK 2 RESOLUTION. 3.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0071 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) : 3.60 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 : 7238 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 375 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) : 3.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 520 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE SET COUNT : 24 REMARK 3 BIN FREE R VALUE : 0.2990 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2268 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 2 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 78.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.01000 REMARK 3 B22 (A**2) : 3.01000 REMARK 3 B33 (A**2) : -6.01000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.539 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.416 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 26.972 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.920 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.857 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2361 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2088 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3211 ; 1.603 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4762 ; 0.861 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 298 ; 8.034 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 99 ;37.375 ;23.030 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 340 ;22.118 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;20.223 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 357 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2692 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 569 ; 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): 1204 ; 5.450 ; 8.323 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1203 ; 5.451 ; 8.321 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1498 ; 8.960 ;12.446 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 : NULL 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 : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5E3U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214302. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-14 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 : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL 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 : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7655 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.600 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 : 13.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.5000 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 77.87850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 44.06700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 44.06700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 116.81775 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 44.06700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 44.06700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 38.93925 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 44.06700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.06700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 116.81775 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 44.06700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.06700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 38.93925 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 77.87850 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: 4340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 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 -88.13400 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 88.13400 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LYS A 56 REMARK 465 PRO A 153 REMARK 465 GLY A 154 REMARK 465 ALA A 155 REMARK 465 SER A 156 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 THR A 402 REMARK 465 VAL A 403 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 63 CE NZ REMARK 470 LEU A 68 CG CD1 CD2 REMARK 470 LYS A 80 CG CD CE NZ REMARK 470 ILE A 96 CD1 REMARK 470 SER A 105 OG REMARK 470 THR A 106 OG1 CG2 REMARK 470 HIS A 110 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 115 CG CD CE NZ REMARK 470 LYS A 117 CD CE NZ REMARK 470 GLU A 149 CG CD OE1 OE2 REMARK 470 SER A 151 OG REMARK 470 ASN A 152 CG OD1 ND2 REMARK 470 SER A 158 OG REMARK 470 LEU A 159 CG CD1 CD2 REMARK 470 GLN A 174 CD OE1 NE2 REMARK 470 LYS A 176 CG CD CE NZ REMARK 470 ARG A 197 NE CZ NH1 NH2 REMARK 470 ASP A 212 CG OD1 OD2 REMARK 470 LYS A 214 CG CD CE NZ REMARK 470 VAL A 229 CG1 CG2 REMARK 470 LEU A 233 CG CD1 CD2 REMARK 470 LYS A 234 CD CE NZ REMARK 470 TYR A 242 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 243 CG CD CE NZ REMARK 470 ARG A 245 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 249 CG CD CE NZ REMARK 470 SER A 252 OG REMARK 470 LYS A 253 CG CD CE NZ REMARK 470 VAL A 255 CG1 CG2 REMARK 470 GLN A 265 CG CD OE1 NE2 REMARK 470 GLU A 269 CG CD OE1 OE2 REMARK 470 LEU A 272 CG CD1 CD2 REMARK 470 GLU A 274 CD OE1 OE2 REMARK 470 LYS A 296 CG CD CE NZ REMARK 470 ILE A 306 CG1 CG2 CD1 REMARK 470 ILE A 308 CG1 CG2 CD1 REMARK 470 HIS A 310 CG ND1 CD2 CE1 NE2 REMARK 470 MET A 357 CG SD CE REMARK 470 PHE A 363 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 366 CG CD CE NZ REMARK 470 GLU A 368 CG CD OE1 OE2 REMARK 470 ARG A 369 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 371 CG CD1 CD2 REMARK 470 GLN A 381 OE1 NE2 REMARK 470 SER A 382 OG REMARK 470 TYR A 383 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 384 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 417 CG CD CE NZ REMARK 470 LYS A 426 CG CD CE NZ REMARK 470 SER A 427 OG 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 O1G ANP A 501 MN MN A 503 1.70 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 THR A 58 47.30 -86.91 REMARK 500 SER A 78 -4.68 -59.27 REMARK 500 GLN A 79 -81.42 -65.78 REMARK 500 ASP A 89 -12.78 -49.83 REMARK 500 SER A 105 -54.69 173.93 REMARK 500 HIS A 109 -89.24 120.05 REMARK 500 HIS A 110 66.96 33.23 REMARK 500 HIS A 111 -24.74 -150.13 REMARK 500 GLU A 145 119.42 -177.53 REMARK 500 SER A 158 105.73 102.57 REMARK 500 ASP A 166 14.99 59.21 REMARK 500 GLN A 194 -51.56 -136.85 REMARK 500 ASP A 212 -120.25 66.90 REMARK 500 ALA A 228 -75.08 -38.79 REMARK 500 HIS A 232 -70.01 -87.19 REMARK 500 THR A 241 -26.00 -141.09 REMARK 500 ARG A 244 45.06 -94.13 REMARK 500 PRO A 248 -55.49 -29.90 REMARK 500 VAL A 255 67.83 -103.37 REMARK 500 TYR A 258 -148.19 -83.99 REMARK 500 MET A 267 52.15 -159.05 REMARK 500 ASN A 275 -71.65 0.75 REMARK 500 GLN A 293 -71.75 -30.61 REMARK 500 ASP A 299 14.90 46.69 REMARK 500 LYS A 366 -92.09 -63.55 REMARK 500 ASP A 378 71.94 56.18 REMARK 500 TYR A 383 33.77 -56.81 REMARK 500 GLN A 416 -71.38 -56.54 REMARK 500 SER A 421 -56.15 -131.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 108 HIS A 109 146.06 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 MN A 502 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 378 OD1 REMARK 620 2 ASP A 378 OD2 59.3 REMARK 620 3 ANP A 501 O2G 132.7 88.3 REMARK 620 4 ANP A 501 O1B 82.8 87.1 60.4 REMARK 620 5 HOH A 602 O 88.2 146.9 113.0 82.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 503 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 378 OD2 REMARK 620 2 ANP A 501 O2A 98.4 REMARK 620 3 HOH A 601 O 138.7 83.3 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 ANP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SE4 A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SE4 A 505 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5E3S RELATED DB: PDB REMARK 900 RELATED ID: 5E3T RELATED DB: PDB DBREF 5E3U A 56 427 UNP Q503I3 Q503I3_DANRE 56 427 SEQRES 1 A 372 LYS THR THR SER SER ALA LEU LYS GLY ALA ILE GLN LEU SEQRES 2 A 372 GLY ILE THR HIS SER VAL GLY SER LEU SER GLN LYS PRO SEQRES 3 A 372 GLU ARG ASP VAL LEU MET GLN ASP PHE GLU VAL VAL GLU SEQRES 4 A 372 SER ILE PHE PHE PRO SER GLN GLY SER SER SER THR PRO SEQRES 5 A 372 GLY HIS HIS HIS GLY ASP PHE LYS PHE LYS THR TYR ALA SEQRES 6 A 372 PRO ILE ALA PHE ARG TYR PHE ARG GLU MET PHE GLY ILE SEQRES 7 A 372 ARG PRO ASP ASP TYR LEU TYR SER LEU CYS ASN GLU PRO SEQRES 8 A 372 LEU ILE GLU LEU SER ASN PRO GLY ALA SER GLY SER LEU SEQRES 9 A 372 PHE TYR VAL SER SER ASP ASP GLU PHE ILE ILE LYS THR SEQRES 10 A 372 VAL GLN HIS LYS GLU ALA GLU PHE LEU GLN THR LEU LEU SEQRES 11 A 372 PRO GLY TYR PHE MET ASN LEU ASN GLN ASN MET ARG THR SEQRES 12 A 372 LEU LEU PRO LYS PHE TYR GLY LEU TYR CYS VAL GLN ALA SEQRES 13 A 372 ASP GLY LYS ASN ILE ARG ILE VAL VAL MET ASN ASN LEU SEQRES 14 A 372 LEU PRO ARG ALA VAL PRO MET HIS LEU LYS PHE ASP LEU SEQRES 15 A 372 LYS GLY SER THR TYR LYS ARG ARG ALA SER PRO LYS GLU SEQRES 16 A 372 ARG SER LYS GLY VAL PRO THR TYR LYS ASP LEU ASP PHE SEQRES 17 A 372 MET GLN ASP MET PRO GLU GLY ILE LEU LEU GLU ASN ASP SEQRES 18 A 372 HIS TYR THR ALA LEU SER ARG THR MET GLN ARG ASP CYS SEQRES 19 A 372 ARG VAL LEU GLN SER PHE LYS ILE MET ASP TYR SER LEU SEQRES 20 A 372 LEU VAL GLY ILE HIS ILE LEU HIS ARG ALA GLY GLU GLU SEQRES 21 A 372 ALA SER THR ALA VAL PRO ASP THR GLN LYS LYS GLY GLN SEQRES 22 A 372 GLY GLN LYS PRO LEU TYR CYS THR ALA ILE GLU SER ILE SEQRES 23 A 372 GLN GLY GLU SER LYS SER LYS THR SER PRO GLN PRO TYR SEQRES 24 A 372 GLU SER MET GLY GLY ILE PRO ALA PHE ASN SER LYS GLY SEQRES 25 A 372 GLU ARG LEU LEU VAL PHE ILE GLY ILE ILE ASP ILE LEU SEQRES 26 A 372 GLN SER TYR ARG LEU VAL LYS LYS LEU GLU HIS SER TRP SEQRES 27 A 372 LYS ALA LEU LEU HIS ASP GLY ASP THR VAL SER VAL HIS SEQRES 28 A 372 ARG PRO SER PHE TYR ALA ASP ARG PHE GLN LYS PHE MET SEQRES 29 A 372 CYS SER THR VAL PHE ARG LYS SER HET ANP A 501 31 HET MN A 502 1 HET MN A 503 1 HET SE4 A 504 5 HET SE4 A 505 5 HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM MN MANGANESE (II) ION HETNAM SE4 SELENATE ION FORMUL 2 ANP C10 H17 N6 O12 P3 FORMUL 3 MN 2(MN 2+) FORMUL 5 SE4 2(O4 SE 2-) FORMUL 7 HOH *2(H2 O) HELIX 1 AA1 THR A 58 LYS A 80 1 23 HELIX 2 AA2 LEU A 86 VAL A 92 1 7 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 THR A 422 1 17 SHEET 1 AA1 3 VAL A 93 GLU A 94 0 SHEET 2 AA1 3 PHE A 114 TYR A 119 -1 O THR A 118 N GLU A 94 SHEET 3 AA1 3 PHE A 97 PHE A 98 -1 N PHE A 98 O PHE A 114 SHEET 1 AA2 5 VAL A 93 GLU A 94 0 SHEET 2 AA2 5 PHE A 114 TYR A 119 -1 O THR A 118 N GLU A 94 SHEET 3 AA2 5 PHE A 203 ALA A 211 -1 O CYS A 208 N LYS A 117 SHEET 4 AA2 5 LYS A 214 ASN A 222 -1 O ILE A 218 N TYR A 207 SHEET 5 AA2 5 PHE A 168 VAL A 173 -1 N ILE A 169 O MET A 221 SHEET 1 AA3 2 ILE A 148 GLU A 149 0 SHEET 2 AA3 2 TYR A 161 VAL A 162 -1 O VAL A 162 N ILE A 148 SHEET 1 AA4 5 THR A 257 LYS A 259 0 SHEET 2 AA4 5 LEU A 233 LEU A 237 1 N LYS A 234 O TYR A 258 SHEET 3 AA4 5 SER A 301 ILE A 306 -1 O VAL A 304 N PHE A 235 SHEET 4 AA4 5 LEU A 370 ILE A 377 -1 O PHE A 373 N GLY A 305 SHEET 5 AA4 5 ILE A 360 ALA A 362 -1 N ILE A 360 O VAL A 372 SHEET 1 AA5 2 ILE A 271 LEU A 273 0 SHEET 2 AA5 2 PHE A 424 LYS A 426 1 O ARG A 425 N ILE A 271 LINK OD1 ASP A 378 MN MN A 502 1555 1555 2.39 LINK OD2 ASP A 378 MN MN A 502 1555 1555 1.89 LINK OD2 ASP A 378 MN MN A 503 1555 1555 1.85 LINK O2G ANP A 501 MN MN A 502 1555 1555 2.02 LINK O1B ANP A 501 MN MN A 502 1555 1555 2.53 LINK O2A ANP A 501 MN MN A 503 1555 1555 2.19 LINK MN MN A 502 O HOH A 602 1555 1555 1.94 LINK MN MN A 503 O HOH A 601 1555 1555 1.83 SITE 1 AC1 16 GLY A 157 PHE A 160 ILE A 169 LYS A 171 SITE 2 AC1 16 ASN A 222 ASN A 223 LEU A 224 ASP A 236 SITE 3 AC1 16 THR A 257 ASP A 299 LEU A 303 ASP A 378 SITE 4 AC1 16 MN A 502 MN A 503 HOH A 601 HOH A 602 SITE 1 AC2 5 ASP A 299 ASP A 378 ANP A 501 MN A 503 SITE 2 AC2 5 HOH A 602 SITE 1 AC3 5 ASP A 299 ASP A 378 ANP A 501 MN A 502 SITE 2 AC3 5 HOH A 601 SITE 1 AC4 2 LYS A 238 ARG A 244 SITE 1 AC5 2 ASN A 215 ARG A 217 CRYST1 88.134 88.134 155.757 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 0.011346 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011346 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006420 0.00000