HEADER TRANSFERASE 06-APR-17 5NMM TITLE THE STRUCTURE OF THE POLO-BOX DOMAIN (PBD) OF PLK1 IN COMPLEX WITH TITLE 2 ALPHA-BROMO-3-IODOTOLUENE. 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, PBD1, MITOSIS, SMALL MOLECULE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.L.KUNCIW,M.ROSSMANN,J.E.STOKES,C.DE FUSCO,D.R.SPRING,M.HYVONEN REVDAT 3 13-SEP-23 5NMM 1 JRNL REVDAT 2 29-MAR-23 5NMM 1 JRNL REVDAT 1 21-FEB-18 5NMM 0 JRNL AUTH P.SHARMA,R.MAHEN,M.ROSSMANN,J.E.STOKES,B.HARDWICK, JRNL AUTH 2 D.J.HUGGINS,A.EMERY,D.L.KUNCIW,M.HYVONEN,D.R.SPRING, JRNL AUTH 3 G.J.MCKENZIE,A.R.VENKITARAMAN JRNL TITL A CRYPTIC HYDROPHOBIC POCKET IN THE POLO-BOX DOMAIN OF THE JRNL TITL 2 POLO-LIKE KINASE PLK1 REGULATES SUBSTRATE RECOGNITION AND JRNL TITL 3 MITOTIC CHROMOSOME SEGREGATION. JRNL REF SCI REP V. 9 15930 2019 JRNL REFN ESSN 2045-2322 JRNL PMID 31685831 JRNL DOI 10.1038/S41598-019-50702-2 REMARK 2 REMARK 2 RESOLUTION. 2.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 13878 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.260 REMARK 3 FREE R VALUE TEST SET COUNT : 730 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 46.5323 - 3.4539 0.97 2620 164 0.1707 0.2106 REMARK 3 2 3.4539 - 2.7416 0.99 2679 114 0.1978 0.2440 REMARK 3 3 2.7416 - 2.3950 0.99 2618 149 0.2079 0.2507 REMARK 3 4 2.3950 - 2.1761 0.98 2634 161 0.2309 0.2955 REMARK 3 5 2.1761 - 2.0201 0.97 2597 142 0.2588 0.3276 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.930 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 : 0.005 1765 REMARK 3 ANGLE : 0.868 2390 REMARK 3 CHIRALITY : 0.048 268 REMARK 3 PLANARITY : 0.003 301 REMARK 3 DIHEDRAL : 12.189 642 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 5NMM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-APR-17. REMARK 100 THE DEPOSITION ID IS D_1200004363. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-AUG-15 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 : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13900 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.020 REMARK 200 RESOLUTION RANGE LOW (A) : 46.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.70100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL 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 (%): 38.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM K/NA TARTRATE, 20% PEG3350, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 293K 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 46.52000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 367 REMARK 465 ALA A 368 REMARK 465 HIS A 369 REMARK 465 MET A 370 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 594 REMARK 465 SER A 595 REMARK 465 ALA A 596 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 398 CG CD OE1 OE2 REMARK 470 LYS A 420 CG CD CE NZ REMARK 470 ARG A 507 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 536 CG CD OE1 NE2 REMARK 470 GLU A 555 CG CD OE1 OE2 REMARK 470 LYS A 556 CG CD CE NZ REMARK 470 LYS A 574 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 HH22 ARG A 396 OE2 GLU A 455 29410 1.43 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 LYS A 420 -53.35 -122.41 REMARK 500 ASP A 449 -38.45 -132.20 REMARK 500 HIS A 468 68.65 36.21 REMARK 500 SER A 592 26.25 -79.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8Z5 A 701 DBREF 5NMM A 371 603 UNP P53350 PLK1_HUMAN 371 603 SEQADV 5NMM GLY A 367 UNP P53350 EXPRESSION TAG SEQADV 5NMM ALA A 368 UNP P53350 EXPRESSION TAG SEQADV 5NMM HIS A 369 UNP P53350 EXPRESSION TAG SEQADV 5NMM MET A 370 UNP P53350 EXPRESSION TAG SEQRES 1 A 237 GLY ALA HIS MET ASP CYS HIS LEU SER ASP MET LEU GLN SEQRES 2 A 237 GLN LEU HIS SER VAL ASN ALA SER LYS PRO SER GLU ARG SEQRES 3 A 237 GLY LEU VAL ARG GLN GLU GLU ALA GLU ASP PRO ALA CYS SEQRES 4 A 237 ILE PRO ILE PHE TRP VAL SER LYS TRP VAL ASP TYR SER SEQRES 5 A 237 ASP LYS TYR GLY LEU GLY TYR GLN LEU CYS ASP ASN SER SEQRES 6 A 237 VAL GLY VAL LEU PHE ASN ASP SER THR ARG LEU ILE LEU SEQRES 7 A 237 TYR ASN ASP GLY ASP SER LEU GLN TYR ILE GLU ARG ASP SEQRES 8 A 237 GLY THR GLU SER TYR LEU THR VAL SER SER HIS PRO ASN SEQRES 9 A 237 SER LEU MET LYS LYS ILE THR LEU LEU LYS TYR PHE ARG SEQRES 10 A 237 ASN TYR MET SER GLU HIS LEU LEU LYS ALA GLY ALA ASN SEQRES 11 A 237 ILE THR PRO ARG GLU GLY ASP GLU LEU ALA ARG LEU PRO SEQRES 12 A 237 TYR LEU ARG THR TRP PHE ARG THR ARG SER ALA ILE ILE SEQRES 13 A 237 LEU HIS LEU SER ASN GLY SER VAL GLN ILE ASN PHE PHE SEQRES 14 A 237 GLN ASP HIS THR LYS LEU ILE LEU CYS PRO LEU MET ALA SEQRES 15 A 237 ALA VAL THR TYR ILE ASP GLU LYS ARG ASP PHE ARG THR SEQRES 16 A 237 TYR ARG LEU SER LEU LEU GLU GLU TYR GLY CYS CYS LYS SEQRES 17 A 237 GLU LEU ALA SER ARG LEU ARG TYR ALA ARG THR MET VAL SEQRES 18 A 237 ASP LYS LEU LEU SER SER ARG SER ALA SER ASN ARG LEU SEQRES 19 A 237 LYS ALA SER HET 8Z5 A 701 15 HETNAM 8Z5 ALPHA-BROMO-3-IODOTOLUENE FORMUL 2 8Z5 C7 H6 BR I FORMUL 3 HOH *34(H2 O) HELIX 1 AA1 HIS A 373 SER A 387 1 15 HELIX 2 AA2 LYS A 388 ARG A 392 5 5 HELIX 3 AA3 ARG A 396 GLU A 401 5 6 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 SER A 592 1 20 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 ILE A 522 N PHE A 515 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 ALA A 549 N CYS A 544 SHEET 6 AA2 6 PHE A 559 ARG A 563 -1 O TYR A 562 N VAL A 550 SITE 1 AC1 3 TYR A 417 TYR A 421 PHE A 482 CRYST1 33.360 93.040 35.910 90.00 100.22 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 0.029976 0.000000 0.005404 0.00000 SCALE2 0.000000 0.010748 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028296 0.00000