HEADER CELL CYCLE 24-MAR-25 9QMO TITLE PLK1 PBD APO PROTEIN AT 1.6A COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE PLK1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POLO-LIKE KINASE 1,PLK-1,SERINE/THREONINE-PROTEIN KINASE 13, COMPND 5 STPK13; COMPND 6 EC: 2.7.11.21; COMPND 7 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 KEYWDS PLK1, PBD, CELL CYCLE, CCAN, KINASE, MITOSIS, KINETOCHORE EXPDTA X-RAY DIFFRACTION AUTHOR L.REN,R.GASPER,I.VETTER,A.MUSACCHIO REVDAT 1 25-FEB-26 9QMO 0 JRNL AUTH L.REN,A.MUSACCHIO JRNL TITL PLK1 PBD APO PROTEIN AT 1.6A JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 34104 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1706 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 49.2800 - 3.6600 1.00 2897 153 0.1616 0.1727 REMARK 3 2 3.6600 - 2.9100 1.00 2765 146 0.1819 0.2051 REMARK 3 3 2.9100 - 2.5400 1.00 2710 142 0.1863 0.2496 REMARK 3 4 2.5400 - 2.3100 1.00 2712 143 0.1754 0.2233 REMARK 3 5 2.3100 - 2.1400 1.00 2698 142 0.1719 0.2394 REMARK 3 6 2.1400 - 2.0200 1.00 2668 141 0.1986 0.2507 REMARK 3 7 2.0200 - 1.9100 1.00 2689 140 0.2192 0.2482 REMARK 3 8 1.9100 - 1.8300 1.00 2655 140 0.2561 0.2836 REMARK 3 9 1.8300 - 1.7600 1.00 2645 139 0.3039 0.3063 REMARK 3 10 1.7600 - 1.7000 1.00 2677 141 0.3413 0.3800 REMARK 3 11 1.7000 - 1.6500 1.00 2647 140 0.3732 0.4090 REMARK 3 12 1.6500 - 1.6000 1.00 2635 139 0.4116 0.4621 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.570 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 : 0.009 1976 REMARK 3 ANGLE : 0.993 2680 REMARK 3 CHIRALITY : 0.055 293 REMARK 3 PLANARITY : 0.010 343 REMARK 3 DIHEDRAL : 16.741 745 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 9QMO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1292145575. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9998578718850196 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34122 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 49.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : 0.14200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.8100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 2.82800 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 (%): 41.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M NA2H(PO4), 20%PEG3350, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 38.35000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.28500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.35000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.28500 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 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 GLY A 343 REMARK 465 SER A 344 REMARK 465 LYS A 345 REMARK 465 GLY A 346 REMARK 465 LEU A 347 REMARK 465 GLU A 348 REMARK 465 ASN A 349 REMARK 465 PRO A 350 REMARK 465 LEU A 351 REMARK 465 PRO A 352 REMARK 465 GLU A 353 REMARK 465 ARG A 354 REMARK 465 PRO A 355 REMARK 465 ARG A 356 REMARK 465 GLU A 357 REMARK 465 LYS A 358 REMARK 465 GLU A 359 REMARK 465 GLU A 360 REMARK 465 PRO A 361 REMARK 465 VAL A 362 REMARK 465 VAL A 363 REMARK 465 ARG A 364 REMARK 465 GLU A 365 REMARK 465 THR A 366 REMARK 465 GLY A 367 REMARK 465 SER A 597 REMARK 465 ASN A 598 REMARK 465 ARG A 599 REMARK 465 LEU A 600 REMARK 465 LYS A 601 REMARK 465 ALA A 602 REMARK 465 SER A 603 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O2 GOL A 702 O HOH A 801 1.98 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 402 81.69 -152.18 REMARK 500 TYR A 417 40.51 -108.39 REMARK 500 ASN A 430 5.55 80.13 REMARK 500 ASP A 449 -34.49 -133.47 REMARK 500 GLU A 501 153.16 -48.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9FJG RELATED DB: PDB REMARK 900 RELATED ID: 9FJH RELATED DB: PDB REMARK 900 RELATED ID: 9FJI RELATED DB: PDB REMARK 900 RELATED ID: 9FJJ RELATED DB: PDB DBREF 9QMO A 345 603 UNP P53350 PLK1_HUMAN 345 603 SEQADV 9QMO GLY A 343 UNP P53350 EXPRESSION TAG SEQADV 9QMO SER A 344 UNP P53350 EXPRESSION TAG SEQRES 1 A 261 GLY SER LYS GLY LEU GLU ASN PRO LEU PRO GLU ARG PRO SEQRES 2 A 261 ARG GLU LYS GLU GLU PRO VAL VAL ARG GLU THR GLY GLU SEQRES 3 A 261 VAL VAL ASP CYS HIS LEU SER ASP MET LEU GLN GLN LEU SEQRES 4 A 261 HIS SER VAL ASN ALA SER LYS PRO SER GLU ARG GLY LEU SEQRES 5 A 261 VAL ARG GLN GLU GLU ALA GLU ASP PRO ALA CYS ILE PRO SEQRES 6 A 261 ILE PHE TRP VAL SER LYS TRP VAL ASP TYR SER ASP LYS SEQRES 7 A 261 TYR GLY LEU GLY TYR GLN LEU CYS ASP ASN SER VAL GLY SEQRES 8 A 261 VAL LEU PHE ASN ASP SER THR ARG LEU ILE LEU TYR ASN SEQRES 9 A 261 ASP GLY ASP SER LEU GLN TYR ILE GLU ARG ASP GLY THR SEQRES 10 A 261 GLU SER TYR LEU THR VAL SER SER HIS PRO ASN SER LEU SEQRES 11 A 261 MET LYS LYS ILE THR LEU LEU LYS TYR PHE ARG ASN TYR SEQRES 12 A 261 MET SER GLU HIS LEU LEU LYS ALA GLY ALA ASN ILE THR SEQRES 13 A 261 PRO ARG GLU GLY ASP GLU LEU ALA ARG LEU PRO TYR LEU SEQRES 14 A 261 ARG THR TRP PHE ARG THR ARG SER ALA ILE ILE LEU HIS SEQRES 15 A 261 LEU SER ASN GLY SER VAL GLN ILE ASN PHE PHE GLN ASP SEQRES 16 A 261 HIS THR LYS LEU ILE LEU CYS PRO LEU MET ALA ALA VAL SEQRES 17 A 261 THR TYR ILE ASP GLU LYS ARG ASP PHE ARG THR TYR ARG SEQRES 18 A 261 LEU SER LEU LEU GLU GLU TYR GLY CYS CYS LYS GLU LEU SEQRES 19 A 261 ALA SER ARG LEU ARG TYR ALA ARG THR MET VAL ASP LYS SEQRES 20 A 261 LEU LEU SER SER ARG SER ALA SER ASN ARG LEU LYS ALA SEQRES 21 A 261 SER HET PO4 A 701 5 HET GOL A 702 14 HET GOL A 703 14 HETNAM PO4 PHOSPHATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 PO4 O4 P 3- FORMUL 3 GOL 2(C3 H8 O3) FORMUL 5 HOH *89(H2 O) HELIX 1 AA1 ASP A 371 SER A 387 1 17 HELIX 2 AA2 ARG A 396 GLU A 401 5 6 HELIX 3 AA3 ASP A 402 ILE A 406 5 5 HELIX 4 AA4 LEU A 472 LEU A 490 1 19 HELIX 5 AA5 LEU A 564 GLY A 571 1 8 HELIX 6 AA6 CYS A 573 ALA A 596 1 24 SHEET 1 AA1 6 VAL A 411 ASP A 416 0 SHEET 2 AA1 6 GLY A 422 LEU A 427 -1 O GLY A 424 N VAL A 415 SHEET 3 AA1 6 VAL A 432 PHE A 436 -1 O GLY A 433 N TYR A 425 SHEET 4 AA1 6 ARG A 441 LEU A 444 -1 O LEU A 444 N VAL A 432 SHEET 5 AA1 6 SER A 450 ILE A 454 -1 O ILE A 454 N ARG A 441 SHEET 6 AA1 6 GLU A 460 THR A 464 -1 O LEU A 463 N LEU A 451 SHEET 1 AA2 6 LEU A 511 ARG A 516 0 SHEET 2 AA2 6 ALA A 520 LEU A 525 -1 O HIS A 524 N THR A 513 SHEET 3 AA2 6 VAL A 530 PHE A 534 -1 O GLN A 531 N LEU A 523 SHEET 4 AA2 6 LYS A 540 CYS A 544 -1 O LEU A 543 N VAL A 530 SHEET 5 AA2 6 ALA A 549 ILE A 553 -1 O ILE A 553 N LYS A 540 SHEET 6 AA2 6 PHE A 559 ARG A 563 -1 O TYR A 562 N VAL A 550 CRYST1 76.700 98.570 33.230 90.00 90.00 90.00 P 21 21 2 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 0.013038 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010145 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030093 0.00000 CONECT 3816 3817 3818 3819 3820 CONECT 3817 3816 CONECT 3818 3816 CONECT 3819 3816 CONECT 3820 3816 CONECT 3821 3822 3823 3827 3828 CONECT 3822 3821 3829 CONECT 3823 3821 3824 3825 3830 CONECT 3824 3823 3831 CONECT 3825 3823 3826 3832 3833 CONECT 3826 3825 3834 CONECT 3827 3821 CONECT 3828 3821 CONECT 3829 3822 CONECT 3830 3823 CONECT 3831 3824 CONECT 3832 3825 CONECT 3833 3825 CONECT 3834 3826 CONECT 3835 3836 3837 3841 3842 CONECT 3836 3835 3843 CONECT 3837 3835 3838 3839 3844 CONECT 3838 3837 3845 CONECT 3839 3837 3840 3846 3847 CONECT 3840 3839 3848 CONECT 3841 3835 CONECT 3842 3835 CONECT 3843 3836 CONECT 3844 3837 CONECT 3845 3838 CONECT 3846 3839 CONECT 3847 3839 CONECT 3848 3840 MASTER 280 0 3 6 12 0 0 6 1962 1 33 21 END