HEADER TRANSFERASE 31-JAN-08 3C5L TITLE POLO-LIKE KINASE 1 POLO BOX DOMAIN IN COMPLEX WITH PPHSPT PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE PLK1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: POLO BOX 1, POLO BOX 2, UNP RESIDUES 373-593; COMPND 5 SYNONYM: POLO-LIKE KINASE 1, PLK-1, SERINE/THREONINE-PROTEIN KINASE COMPND 6 13, STPK13; COMPND 7 EC: 2.7.11.21; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: PEPTIDE; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PLK1, PLK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS PLK1, POLO-LIKE KINASE 1, POLO BOX DOMAIN, PHOSPHOPEPTIDE, ATP- KEYWDS 2 BINDING, NUCLEOTIDE-BINDING, NUCLEUS, PHOSPHOPROTEIN, KEYWDS 3 SERINE/THREONINE-PROTEIN KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.C.LIM,M.B.YAFFE REVDAT 4 20-NOV-24 3C5L 1 REMARK REVDAT 3 30-AUG-23 3C5L 1 LINK REVDAT 2 25-AUG-09 3C5L 1 JRNL REVDAT 1 17-FEB-09 3C5L 0 JRNL AUTH S.M.YUN,T.MOULAEI,D.LIM,J.K.BANG,J.E.PARK,S.R.SHENOY,F.LIU, JRNL AUTH 2 Y.H.KANG,C.LIAO,N.K.SOUNG,S.LEE,D.Y.YOON,Y.LIM,D.H.LEE, JRNL AUTH 3 A.OTAKA,E.APPELLA,J.B.MCMAHON,M.C.NICKLAUS,T.R.BURKE, JRNL AUTH 4 M.B.YAFFE,A.WLODAWER,K.S.LEE JRNL TITL STRUCTURAL AND FUNCTIONAL ANALYSES OF MINIMAL JRNL TITL 2 PHOSPHOPEPTIDES TARGETING THE POLO-BOX DOMAIN OF POLO-LIKE JRNL TITL 3 KINASE 1. JRNL REF NAT.STRUCT.MOL.BIOL. V. 16 876 2009 JRNL REFN ISSN 1545-9993 JRNL PMID 19597481 JRNL DOI 10.1038/NSMB.1628 REMARK 2 REMARK 2 RESOLUTION. 2.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.61 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 612513.780 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.8 REMARK 3 NUMBER OF REFLECTIONS : 10186 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 SET) : 0.246 REMARK 3 FREE R VALUE : 0.293 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 529 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.013 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.33 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.48 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 59.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1032 REMARK 3 BIN R VALUE (WORKING SET) : 0.3500 REMARK 3 BIN FREE R VALUE : 0.4480 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 49 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.064 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1810 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 35 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.45000 REMARK 3 B22 (A**2) : 10.38000 REMARK 3 B33 (A**2) : -12.83000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : 0.35 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.45 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.49 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.940 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.850 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.760 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.670 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.710 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 40.26 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3C5L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1000046369. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 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 : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10764 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.330 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : 0.05100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 27.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.26800 REMARK 200 R SYM FOR SHELL (I) : 0.26800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: PDB ENTRY 1UMW, CHAIN A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, PH 6, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 17.72100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.90850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.24750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.90850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.72100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.24750 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 300 REMARK: 1 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 820 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 ASP A 503 REMARK 465 GLU A 504 REMARK 465 LEU A 505 REMARK 465 ALA A 506 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 GLU A 391 41.63 -89.60 REMARK 500 ARG A 396 65.98 -111.22 REMARK 500 PRO A 403 -34.48 -36.79 REMARK 500 CYS A 405 28.79 -79.17 REMARK 500 TYR A 421 -59.50 -121.30 REMARK 500 ASN A 430 -2.91 78.69 REMARK 500 ASN A 446 2.27 -65.03 REMARK 500 ASP A 457 4.10 -53.76 REMARK 500 THR A 459 94.52 -65.75 REMARK 500 ASN A 496 33.68 -90.99 REMARK 500 GLN A 536 -70.59 -42.01 REMARK 500 REMARK 500 REMARK: NULL DBREF 3C5L A 373 593 UNP P53350 PLK1_HUMAN 373 593 DBREF 3C5L B 1 5 PDB 3C5L 3C5L 1 5 SEQRES 1 A 221 HIS LEU SER ASP MET LEU GLN GLN LEU HIS SER VAL ASN SEQRES 2 A 221 ALA SER LYS PRO SER GLU ARG GLY LEU VAL ARG GLN GLU SEQRES 3 A 221 GLU ALA GLU ASP PRO ALA CYS ILE PRO ILE PHE TRP VAL SEQRES 4 A 221 SER LYS TRP VAL ASP TYR SER ASP LYS TYR GLY LEU GLY SEQRES 5 A 221 TYR GLN LEU CYS ASP ASN SER VAL GLY VAL LEU PHE ASN SEQRES 6 A 221 ASP SER THR ARG LEU ILE LEU TYR ASN ASP GLY ASP SER SEQRES 7 A 221 LEU GLN TYR ILE GLU ARG ASP GLY THR GLU SER TYR LEU SEQRES 8 A 221 THR VAL SER SER HIS PRO ASN SER LEU MET LYS LYS ILE SEQRES 9 A 221 THR LEU LEU LYS TYR PHE ARG ASN TYR MET SER GLU HIS SEQRES 10 A 221 LEU LEU LYS ALA GLY ALA ASN ILE THR PRO ARG GLU GLY SEQRES 11 A 221 ASP GLU LEU ALA ARG LEU PRO TYR LEU ARG THR TRP PHE SEQRES 12 A 221 ARG THR ARG SER ALA ILE ILE LEU HIS LEU SER ASN GLY SEQRES 13 A 221 SER VAL GLN ILE ASN PHE PHE GLN ASP HIS THR LYS LEU SEQRES 14 A 221 ILE LEU CYS PRO LEU MET ALA ALA VAL THR TYR ILE ASP SEQRES 15 A 221 GLU LYS ARG ASP PHE ARG THR TYR ARG LEU SER LEU LEU SEQRES 16 A 221 GLU GLU TYR GLY CYS CYS LYS GLU LEU ALA SER ARG LEU SEQRES 17 A 221 ARG TYR ALA ARG THR MET VAL ASP LYS LEU LEU SER SER SEQRES 1 B 5 PRO PRO HIS SER TPO MODRES 3C5L TPO B 5 THR PHOSPHOTHREONINE HET TPO B 5 12 HETNAM TPO PHOSPHOTHREONINE HETSYN TPO PHOSPHONOTHREONINE FORMUL 2 TPO C4 H10 N O6 P FORMUL 3 HOH *35(H2 O) HELIX 1 1 HIS A 373 SER A 387 1 15 HELIX 2 2 ARG A 396 GLU A 401 5 6 HELIX 3 3 ASP A 402 ILE A 406 5 5 HELIX 4 4 SER A 466 HIS A 468 5 3 HELIX 5 5 PRO A 469 SER A 471 5 3 HELIX 6 6 LEU A 472 LEU A 490 1 19 HELIX 7 7 LEU A 564 GLU A 568 1 5 HELIX 8 8 CYS A 573 SER A 592 1 20 SHEET 1 A 6 VAL A 411 ASP A 416 0 SHEET 2 A 6 GLY A 422 LEU A 427 -1 O GLN A 426 N SER A 412 SHEET 3 A 6 VAL A 432 PHE A 436 -1 O LEU A 435 N LEU A 423 SHEET 4 A 6 ARG A 441 LEU A 444 -1 O LEU A 444 N VAL A 432 SHEET 5 A 6 SER A 450 ILE A 454 -1 O ILE A 454 N ARG A 441 SHEET 6 A 6 GLU A 460 THR A 464 -1 O LEU A 463 N LEU A 451 SHEET 1 B 6 LEU A 511 THR A 517 0 SHEET 2 B 6 ALA A 520 LEU A 525 -1 O ILE A 522 N PHE A 515 SHEET 3 B 6 VAL A 530 PHE A 534 -1 O GLN A 531 N LEU A 523 SHEET 4 B 6 LYS A 540 CYS A 544 -1 O LEU A 543 N VAL A 530 SHEET 5 B 6 ALA A 549 ILE A 553 -1 O ILE A 553 N LYS A 540 SHEET 6 B 6 PHE A 559 ARG A 563 -1 O ARG A 560 N TYR A 552 LINK C SER B 4 N TPO B 5 1555 1555 1.33 CRYST1 35.442 66.495 105.817 90.00 90.00 90.00 P 21 21 21 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 0.028215 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015039 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009450 0.00000