HEADER CELL CYCLE 08-JUN-23 8JOQ TITLE PLK1 POLO-BOX DOMAIN BOUND TO HPV18 L2 RESIDUES 209-215 WITH PTHR213 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE PLK1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: POLO-BOX DOMAIN; COMPND 5 SYNONYM: POLO-LIKE KINASE 1,PLK-1,SERINE/THREONINE-PROTEIN KINASE 13, COMPND 6 STPK13; COMPND 7 EC: 2.7.11.21; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: HPV18 L2 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 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HUMAN PAPILLOMAVIRUS 18; SOURCE 11 ORGANISM_TAXID: 333761 KEYWDS PLK1, POLO-BOX DOMAIN, PBD, HPV, L2, HPV18, REPLICATION, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR B.KU,S.JUNG REVDAT 2 18-OCT-23 8JOQ 1 JRNL REVDAT 1 11-OCT-23 8JOQ 0 JRNL AUTH S.JUNG,H.S.LEE,H.C.SHIN,J.S.CHOI,S.J.KIM,B.KU JRNL TITL CRYSTAL STRUCTURES OF PLK1 POLO-BOX DOMAIN BOUND TO THE JRNL TITL 2 HUMAN PAPILLOMAVIRUS MINOR CAPSID PROTEIN L2-DERIVED JRNL TITL 3 PEPTIDE. JRNL REF J.MICROBIOL V. 61 755 2023 JRNL REFN ESSN 1976-3794 JRNL PMID 37684534 JRNL DOI 10.1007/S12275-023-00071-3 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 18520 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1867 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 35.1410 - 4.2210 0.99 1433 155 0.1624 0.2149 REMARK 3 2 4.2210 - 3.3512 0.79 1127 126 0.1832 0.2167 REMARK 3 3 3.3512 - 2.9278 0.99 1390 148 0.2099 0.2543 REMARK 3 4 2.9278 - 2.6602 0.99 1410 160 0.2257 0.2506 REMARK 3 5 2.6602 - 2.4696 0.99 1383 141 0.2263 0.2600 REMARK 3 6 2.4696 - 2.3240 0.99 1381 163 0.2310 0.2548 REMARK 3 7 2.3240 - 2.2077 0.61 833 110 0.2154 0.2706 REMARK 3 8 2.2077 - 2.1116 0.99 1376 165 0.2181 0.2545 REMARK 3 9 2.1116 - 2.0303 0.99 1374 159 0.2325 0.2763 REMARK 3 10 2.0303 - 1.9602 0.98 1359 142 0.2307 0.3062 REMARK 3 11 1.9602 - 1.8990 0.71 1013 105 0.2524 0.3337 REMARK 3 12 1.8990 - 1.8447 0.93 1262 145 0.2437 0.2970 REMARK 3 13 1.8447 - 1.7961 0.94 1312 148 0.2428 0.3415 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.390 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 1864 REMARK 3 ANGLE : 0.891 2522 REMARK 3 CHIRALITY : 0.056 281 REMARK 3 PLANARITY : 0.006 317 REMARK 3 DIHEDRAL : 19.744 1131 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 8JOQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1300038490. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAR-23 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : NULL 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) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18536 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.796 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04500 REMARK 200 FOR THE DATA SET : 5.5000 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 (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.19900 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MALATE MES TRIS BUFFER PH 6.5, REMARK 280 25% POLYETHYLENE GLYCOL 1500, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K 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 27.17300 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: 1020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 GLY A 369 REMARK 465 HIS A 370 REMARK 465 ASP A 371 REMARK 465 CYS A 372 REMARK 465 GLY A 502 REMARK 465 ASP A 503 REMARK 465 GLU A 504 REMARK 465 LEU A 505 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 ARG A 560 CD NE CZ NH1 NH2 REMARK 470 ARG A 594 NE CZ NH1 NH2 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 -50.59 -126.38 REMARK 500 ASP A 449 -42.22 -136.03 REMARK 500 SER B 212 -177.71 -69.35 REMARK 500 REMARK 500 REMARK: NULL DBREF 8JOQ A 371 594 UNP P53350 PLK1_HUMAN 371 594 DBREF 8JOQ B 209 215 UNP P06793 VL2_HPV18 209 215 SEQADV 8JOQ GLY A 369 UNP P53350 EXPRESSION TAG SEQADV 8JOQ HIS A 370 UNP P53350 EXPRESSION TAG SEQRES 1 A 226 GLY HIS ASP CYS HIS LEU SER ASP MET LEU GLN GLN LEU SEQRES 2 A 226 HIS SER VAL ASN ALA SER LYS PRO SER GLU ARG GLY LEU SEQRES 3 A 226 VAL ARG GLN GLU GLU ALA GLU ASP PRO ALA CYS ILE PRO SEQRES 4 A 226 ILE PHE TRP VAL SER LYS TRP VAL ASP TYR SER ASP LYS SEQRES 5 A 226 TYR GLY LEU GLY TYR GLN LEU CYS ASP ASN SER VAL GLY SEQRES 6 A 226 VAL LEU PHE ASN ASP SER THR ARG LEU ILE LEU TYR ASN SEQRES 7 A 226 ASP GLY ASP SER LEU GLN TYR ILE GLU ARG ASP GLY THR SEQRES 8 A 226 GLU SER TYR LEU THR VAL SER SER HIS PRO ASN SER LEU SEQRES 9 A 226 MET LYS LYS ILE THR LEU LEU LYS TYR PHE ARG ASN TYR SEQRES 10 A 226 MET SER GLU HIS LEU LEU LYS ALA GLY ALA ASN ILE THR SEQRES 11 A 226 PRO ARG GLU GLY ASP GLU LEU ALA ARG LEU PRO TYR LEU SEQRES 12 A 226 ARG THR TRP PHE ARG THR ARG SER ALA ILE ILE LEU HIS SEQRES 13 A 226 LEU SER ASN GLY SER VAL GLN ILE ASN PHE PHE GLN ASP SEQRES 14 A 226 HIS THR LYS LEU ILE LEU CYS PRO LEU MET ALA ALA VAL SEQRES 15 A 226 THR TYR ILE ASP GLU LYS ARG ASP PHE ARG THR TYR ARG SEQRES 16 A 226 LEU SER LEU LEU GLU GLU TYR GLY CYS CYS LYS GLU LEU SEQRES 17 A 226 ALA SER ARG LEU ARG TYR ALA ARG THR MET VAL ASP LYS SEQRES 18 A 226 LEU LEU SER SER ARG SEQRES 1 B 7 PRO ILE SER SER TPO PRO LEU MODRES 8JOQ TPO B 213 THR MODIFIED RESIDUE HET TPO B 213 11 HETNAM TPO PHOSPHOTHREONINE HETSYN TPO PHOSPHONOTHREONINE FORMUL 2 TPO C4 H10 N O6 P FORMUL 3 HOH *117(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 ASP A 402 ILE A 406 5 5 HELIX 5 AA5 PRO A 469 SER A 471 5 3 HELIX 6 AA6 LEU A 472 LEU A 490 1 19 HELIX 7 AA7 LEU A 564 GLY A 571 1 8 HELIX 8 AA8 CYS A 573 SER A 593 1 21 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 LEU A 435 N LEU A 423 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 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 LINK C SER B 212 N TPO B 213 1555 1555 1.33 LINK C TPO B 213 N PRO B 214 1555 1555 1.34 CRYST1 35.143 54.346 57.295 90.00 90.61 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 0.028455 0.000000 0.000304 0.00000 SCALE2 0.000000 0.018401 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017455 0.00000