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 <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
(ATOM LINES ARE NOT SHOWN.)
END
