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 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 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