HEADER TRANSFERASE 31-JAN-08 3C5L TITLE POLO-LIKE KINASE 1 POLO BOX DOMAIN IN COMPLEX WITH PPHSPT TITLE 2 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- COMPND 6 PROTEIN KINASE 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, KEYWDS 2 ATP-BINDING, NUCLEOTIDE-BINDING, NUCLEUS, PHOSPHOPROTEIN, KEYWDS 3 SERINE/THREONINE-PROTEIN KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.C.LIM,M.B.YAFFE 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, JRNL AUTH 2 S.R.SHENOY,F.LIU,Y.H.KANG,C.LIAO,N.K.SOUNG,S.LEE, JRNL AUTH 3 D.Y.YOON,Y.LIM,D.H.LEE,A.OTAKA,E.APPELLA, JRNL AUTH 4 J.B.MCMAHON,M.C.NICKLAUS,T.R.BURKE,M.B.YAFFE, JRNL AUTH 5 A.WLODAWER,K.S.LEE JRNL TITL STRUCTURAL AND FUNCTIONAL ANALYSES OF MINIMAL JRNL TITL 2 PHOSPHOPEPTIDES TARGETING THE POLO-BOX DOMAIN OF JRNL TITL 3 POLO-LIKE 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 1 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) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.94 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. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-FEB-08. REMARK 100 THE RCSB ID CODE IS RCSB046369. 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 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 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 MASTER 255 0 1 8 12 0 0 6 0 0 0 18 END