HEADER TRANSFERASE/PEPTIDE 03-JAN-14 4O9W
TITLE CRYSTAL STRUCTURE OF POLO-LIKE KINASE(PLK1)PBD IN COMPLEX WITH PHOSPHO
TITLE 2 PEPTIDE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE PLK1;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 373-594;
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: PHOSPHO PEPTIDE VAL-LEU-SER-TPO-LEU-NH2;
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 MOL_ID: 2;
SOURCE 9 SYNTHETIC: YES;
SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 11 ORGANISM_COMMON: HUMAN;
SOURCE 12 ORGANISM_TAXID: 9606;
SOURCE 13 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
KEYWDS POLO-BOX DOMAIN, TRANSFERASE-PEPTIDE COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR S.M.BONG,B.I.LEE,K.T.KIM
REVDAT 3 18-DEC-19 4O9W 1 JRNL REMARK LINK
REVDAT 2 26-NOV-14 4O9W 1 REMARK
REVDAT 1 13-AUG-14 4O9W 0
JRNL AUTH J.H.KIM,J.SHIM,M.J.JI,Y.JUNG,S.M.BONG,Y.J.JANG,E.K.YOON,
JRNL AUTH 2 S.J.LEE,K.G.KIM,Y.H.KIM,C.LEE,B.I.LEE,K.T.KIM
JRNL TITL THE CONDENSIN COMPONENT NCAPG2 REGULATES
JRNL TITL 2 MICROTUBULE-KINETOCHORE ATTACHMENT THROUGH RECRUITMENT OF
JRNL TITL 3 POLO-LIKE KINASE 1 TO KINETOCHORES.
JRNL REF NAT COMMUN V. 5 4588 2014
JRNL REFN ESSN 2041-1723
JRNL PMID 25109385
JRNL DOI 10.1038/NCOMMS5588
REMARK 2
REMARK 2 RESOLUTION. 1.69 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309)
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.69
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.03
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380
REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3
REMARK 3 NUMBER OF REFLECTIONS : 21771
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.203
REMARK 3 R VALUE (WORKING SET) : 0.201
REMARK 3 FREE R VALUE : 0.240
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080
REMARK 3 FREE R VALUE TEST SET COUNT : 1107
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 29.0324 - 3.3864 0.95 2660 154 0.1937 0.2329
REMARK 3 2 3.3864 - 2.6885 0.99 2732 154 0.2111 0.2310
REMARK 3 3 2.6885 - 2.3488 0.99 2732 142 0.2120 0.2567
REMARK 3 4 2.3488 - 2.1341 0.99 2719 129 0.1899 0.2295
REMARK 3 5 2.1341 - 1.9812 0.99 2680 143 0.1901 0.2491
REMARK 3 6 1.9812 - 1.8644 0.98 2691 134 0.2006 0.2339
REMARK 3 7 1.8644 - 1.7711 0.95 2581 153 0.2152 0.2632
REMARK 3 8 1.7711 - 1.6940 0.69 1869 98 0.2396 0.3348
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.830
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.007 1797
REMARK 3 ANGLE : 1.110 2430
REMARK 3 CHIRALITY : 0.077 274
REMARK 3 PLANARITY : 0.004 303
REMARK 3 DIHEDRAL : 15.043 667
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 4O9W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JAN-14.
REMARK 100 THE DEPOSITION ID IS D_1000084225.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 15-SEP-13
REMARK 200 TEMPERATURE (KELVIN) : 200
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : PAL/PLS
REMARK 200 BEAMLINE : 5C (4A)
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 : DOUBLE CRYSTAL MONOCHROMATOR
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.694
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7
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: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 38.38
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 200MM POTASSIUM IODIDE, 100MM MES, 25%
REMARK 280 PEG 4000, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,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 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 25.92900
REMARK 290 SMTRY3 2 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 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: 980 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 10890 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL
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 ARG A 392
REMARK 465 GLY A 393
REMARK 465 PRO A 499
REMARK 465 ARG A 500
REMARK 465 GLU A 501
REMARK 465 GLY A 502
REMARK 465 ASP A 503
REMARK 465 GLU A 504
REMARK 465 LEU A 505
REMARK 465 ALA A 506
REMARK 465 ARG A 507
REMARK 480
REMARK 480 ZERO OCCUPANCY ATOM
REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO
REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS
REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 480 M RES C SSEQI ATOMS
REMARK 480 GLN A 536 CD
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 LYS A 420 -49.48 -131.89
REMARK 500 ASP A 449 -37.23 -137.00
REMARK 500
REMARK 500 REMARK: NULL
DBREF 4O9W A 373 594 UNP P53350 PLK1_HUMAN 373 594
DBREF 4O9W B 1 6 PDB 4O9W 4O9W 1 6
SEQRES 1 A 222 HIS LEU SER ASP MET LEU GLN GLN LEU HIS SER VAL ASN
SEQRES 2 A 222 ALA SER LYS PRO SER GLU ARG GLY LEU VAL ARG GLN GLU
SEQRES 3 A 222 GLU ALA GLU ASP PRO ALA CYS ILE PRO ILE PHE TRP VAL
SEQRES 4 A 222 SER LYS TRP VAL ASP TYR SER ASP LYS TYR GLY LEU GLY
SEQRES 5 A 222 TYR GLN LEU CYS ASP ASN SER VAL GLY VAL LEU PHE ASN
SEQRES 6 A 222 ASP SER THR ARG LEU ILE LEU TYR ASN ASP GLY ASP SER
SEQRES 7 A 222 LEU GLN TYR ILE GLU ARG ASP GLY THR GLU SER TYR LEU
SEQRES 8 A 222 THR VAL SER SER HIS PRO ASN SER LEU MET LYS LYS ILE
SEQRES 9 A 222 THR LEU LEU LYS TYR PHE ARG ASN TYR MET SER GLU HIS
SEQRES 10 A 222 LEU LEU LYS ALA GLY ALA ASN ILE THR PRO ARG GLU GLY
SEQRES 11 A 222 ASP GLU LEU ALA ARG LEU PRO TYR LEU ARG THR TRP PHE
SEQRES 12 A 222 ARG THR ARG SER ALA ILE ILE LEU HIS LEU SER ASN GLY
SEQRES 13 A 222 SER VAL GLN ILE ASN PHE PHE GLN ASP HIS THR LYS LEU
SEQRES 14 A 222 ILE LEU CYS PRO LEU MET ALA ALA VAL THR TYR ILE ASP
SEQRES 15 A 222 GLU LYS ARG ASP PHE ARG THR TYR ARG LEU SER LEU LEU
SEQRES 16 A 222 GLU GLU TYR GLY CYS CYS LYS GLU LEU ALA SER ARG LEU
SEQRES 17 A 222 ARG TYR ALA ARG THR MET VAL ASP LYS LEU LEU SER SER
SEQRES 18 A 222 ARG
SEQRES 1 B 6 VAL LEU SER TPO LEU NH2
MODRES 4O9W TPO B 4 THR PHOSPHOTHREONINE
HET TPO B 4 11
HET NH2 B 6 1
HETNAM TPO PHOSPHOTHREONINE
HETNAM NH2 AMINO GROUP
HETSYN TPO PHOSPHONOTHREONINE
FORMUL 2 TPO C4 H10 N O6 P
FORMUL 2 NH2 H2 N
FORMUL 3 HOH *62(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 PRO A 469 SER A 471 5 3
HELIX 5 5 LEU A 472 LEU A 490 1 19
HELIX 6 6 LEU A 564 GLY A 571 1 8
HELIX 7 7 CYS A 573 SER A 593 1 21
SHEET 1 A 6 VAL A 411 ASP A 416 0
SHEET 2 A 6 GLY A 422 LEU A 427 -1 O GLY A 424 N VAL A 415
SHEET 3 A 6 VAL A 432 PHE A 436 -1 O GLY A 433 N TYR A 425
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 ARG A 516 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 ALA A 549 N CYS A 544
SHEET 6 B 6 PHE A 559 ARG A 563 -1 O TYR A 562 N VAL A 550
LINK C SER B 3 N TPO B 4 1555 1555 1.33
LINK C TPO B 4 N LEU B 5 1555 1555 1.33
LINK C LEU B 5 N NH2 B 6 1555 1555 1.33
CRYST1 35.649 51.858 57.654 90.00 100.69 90.00 P 1 21 1 2
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 0.028051 0.000000 0.005295 0.00000
SCALE2 0.000000 0.019283 0.000000 0.00000
SCALE3 0.000000 0.000000 0.017651 0.00000
(ATOM LINES ARE NOT SHOWN.)
END