HEADER SIGNALING PROTEIN, TRANSFERASE 23-JUL-21 7RL3 TITLE STRUCTURE OF DROSOPHILA MELANOGASTER PLK4 PB3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE PLK4; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: POLO BOX DOMAIN; COMPND 5 SYNONYM: POLO-LIKE KINASE 4,PLK-4,SERINE/THREONINE-PROTEIN KINASE COMPND 6 SAK; COMPND 7 EC: 2.7.11.21; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: NATIVE N-TERMINAL CLONING ARTIFACT: GSHM SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: SAK, CG7186; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: B834 KEYWDS KINASE, SAK KINASE, PLK4, POLO BOX, SIGNALING PROTEIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.C.SLEP,L.K.SLEVIN REVDAT 2 16-AUG-23 7RL3 1 JRNL REVDAT 1 03-AUG-22 7RL3 0 JRNL AUTH J.M.RYNIAWEC,D.W.BUSTER,L.K.SLEVIN,C.J.BOESE,A.AMOIROGLOU, JRNL AUTH 2 S.M.DEAN,K.C.SLEP,G.C.ROGERS JRNL TITL POLO-LIKE KINASE 4 HOMODIMERIZATION AND CONDENSATE FORMATION JRNL TITL 2 REGULATE ITS OWN PROTEIN LEVELS BUT ARE NOT REQUIRED FOR JRNL TITL 3 CENTRIOLE ASSEMBLY. JRNL REF MOL.BIOL.CELL V. 34 AR80 2023 JRNL REFN ESSN 1939-4586 JRNL PMID 37163316 JRNL DOI 10.1091/MBC.E22-12-0572 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX V1.8 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.4 REMARK 3 NUMBER OF REFLECTIONS : 14186 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1420 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 39.6170 - 3.7636 1.00 1427 159 0.1893 0.2182 REMARK 3 2 3.7636 - 2.9876 1.00 1413 157 0.1821 0.2287 REMARK 3 3 2.9876 - 2.6101 1.00 1385 154 0.2038 0.2580 REMARK 3 4 2.6101 - 2.3715 0.99 1398 156 0.2026 0.2385 REMARK 3 5 2.3715 - 2.2015 0.99 1373 154 0.1873 0.2170 REMARK 3 6 2.2015 - 2.0717 0.99 1376 152 0.1832 0.2142 REMARK 3 7 2.0717 - 1.9680 0.98 1370 152 0.1902 0.2427 REMARK 3 8 1.9680 - 1.8823 0.90 1262 143 0.1985 0.2596 REMARK 3 9 1.8823 - 1.8098 0.74 1016 113 0.2214 0.2769 REMARK 3 10 1.8098 - 1.7500 0.53 746 80 0.2186 0.2757 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) : 25.550 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.84 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.55 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 : 0.013 1273 REMARK 3 ANGLE : 1.644 1731 REMARK 3 CHIRALITY : 0.099 203 REMARK 3 PLANARITY : 0.009 225 REMARK 3 DIHEDRAL : 15.478 474 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 6.4029 -6.2661 24.7053 REMARK 3 T TENSOR REMARK 3 T11: 0.1771 T22: 0.1855 REMARK 3 T33: 0.1998 T12: 0.0185 REMARK 3 T13: 0.0148 T23: -0.0287 REMARK 3 L TENSOR REMARK 3 L11: 0.4323 L22: 1.1588 REMARK 3 L33: 1.9362 L12: -0.2792 REMARK 3 L13: 0.6171 L23: -0.8911 REMARK 3 S TENSOR REMARK 3 S11: -0.0512 S12: -0.0173 S13: 0.0287 REMARK 3 S21: 0.0828 S22: 0.0608 S23: -0.0093 REMARK 3 S31: -0.0886 S32: -0.0810 S33: -0.0128 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 7RL3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1000258377. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-AUG-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14468 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 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 (%) : 93.4 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 62.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.25100 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: SAD REMARK 200 SOFTWARE USED: PHENIX V1.8 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: D.M. PLK4 PB3 WAS CRYSTALLIZED USING A REMARK 280 MOTHER LIQUOR (1 ML) CONTAINING 32% PEG 4000, 200 MM LI2SO4, AND REMARK 280 200 MM TRIS AT PH 8.5. THE HANGING DROP INITIAL CONDITION WAS 2 REMARK 280 UL MOTHER LIQUOR PLUS 2 UL (15 MG/ML STOCK) PLK4 PB3. CRYSTALS REMARK 280 WERE TRANSFERRED TO A CRYO CONDITION CONTAINING MOTHER LIQUOR REMARK 280 PLUS 20% ETHYLENE GLYCOL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 26.54750 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 653 REMARK 465 SER A 654 REMARK 465 HIS A 655 REMARK 465 MET A 656 REMARK 465 GLN A 657 REMARK 465 ASN A 658 REMARK 465 ILE A 659 REMARK 465 GLY B 653 REMARK 465 SER B 654 REMARK 465 HIS B 655 REMARK 465 MET B 656 REMARK 465 GLN B 657 REMARK 465 ASN B 658 REMARK 465 ILE B 659 REMARK 465 PRO B 694 REMARK 465 SER B 695 REMARK 465 MET B 696 REMARK 465 GLN B 697 REMARK 465 GLY B 698 REMARK 465 GLY B 744 REMARK 465 SER B 745 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 GLU A 668 -25.80 75.43 REMARK 500 ILE A 669 -66.91 -98.52 REMARK 500 GLU B 668 -6.54 75.88 REMARK 500 ILE B 669 -54.11 -120.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 858 DISTANCE = 6.52 ANGSTROMS REMARK 525 HOH B 860 DISTANCE = 6.93 ANGSTROMS DBREF 7RL3 A 657 745 UNP O97143 PLK4_DROME 657 745 DBREF 7RL3 B 657 745 UNP O97143 PLK4_DROME 657 745 SEQADV 7RL3 GLY A 653 UNP O97143 EXPRESSION TAG SEQADV 7RL3 SER A 654 UNP O97143 EXPRESSION TAG SEQADV 7RL3 HIS A 655 UNP O97143 EXPRESSION TAG SEQADV 7RL3 MET A 656 UNP O97143 EXPRESSION TAG SEQADV 7RL3 GLY B 653 UNP O97143 EXPRESSION TAG SEQADV 7RL3 SER B 654 UNP O97143 EXPRESSION TAG SEQADV 7RL3 HIS B 655 UNP O97143 EXPRESSION TAG SEQADV 7RL3 MET B 656 UNP O97143 EXPRESSION TAG SEQRES 1 A 93 GLY SER HIS MET GLN ASN ILE PRO ILE LYS ARG ILE ASN SEQRES 2 A 93 VAL PRO GLU ILE GLY ILE ALA THR GLU LEU SER HIS GLY SEQRES 3 A 93 VAL VAL GLN VAL GLN PHE TYR ASP GLY SER VAL VAL SER SEQRES 4 A 93 VAL ILE PRO SER MET GLN GLY GLY GLY ILE THR TYR THR SEQRES 5 A 93 GLN PRO ASN GLY THR SER THR HIS PHE GLY LYS GLY ASP SEQRES 6 A 93 ASP LEU PRO PHE PRO VAL ARG ASP ARG VAL GLY GLN ILE SEQRES 7 A 93 PRO ASN ILE GLN LEU LYS LEU LYS THR ALA PRO LEU LEU SEQRES 8 A 93 GLY SER SEQRES 1 B 93 GLY SER HIS MET GLN ASN ILE PRO ILE LYS ARG ILE ASN SEQRES 2 B 93 VAL PRO GLU ILE GLY ILE ALA THR GLU LEU SER HIS GLY SEQRES 3 B 93 VAL VAL GLN VAL GLN PHE TYR ASP GLY SER VAL VAL SER SEQRES 4 B 93 VAL ILE PRO SER MET GLN GLY GLY GLY ILE THR TYR THR SEQRES 5 B 93 GLN PRO ASN GLY THR SER THR HIS PHE GLY LYS GLY ASP SEQRES 6 B 93 ASP LEU PRO PHE PRO VAL ARG ASP ARG VAL GLY GLN ILE SEQRES 7 B 93 PRO ASN ILE GLN LEU LYS LEU LYS THR ALA PRO LEU LEU SEQRES 8 B 93 GLY SER FORMUL 3 HOH *118(H2 O) HELIX 1 AA1 PRO A 720 GLY A 728 1 9 HELIX 2 AA2 GLN A 729 ALA A 740 1 12 HELIX 3 AA3 PRO B 720 GLY B 728 1 9 HELIX 4 AA4 GLN B 729 ALA B 740 1 12 SHEET 1 AA1 6 LYS A 662 VAL A 666 0 SHEET 2 AA1 6 GLY A 670 GLU A 674 -1 O GLY A 670 N VAL A 666 SHEET 3 AA1 6 VAL A 680 PHE A 684 -1 O GLN A 683 N ILE A 671 SHEET 4 AA1 6 VAL A 689 VAL A 692 -1 O VAL A 690 N VAL A 682 SHEET 5 AA1 6 ILE A 701 THR A 704 -1 O THR A 702 N SER A 691 SHEET 6 AA1 6 SER A 710 PHE A 713 -1 O PHE A 713 N ILE A 701 SHEET 1 AA2 6 LYS B 662 VAL B 666 0 SHEET 2 AA2 6 GLY B 670 GLU B 674 -1 O GLY B 670 N VAL B 666 SHEET 3 AA2 6 VAL B 680 PHE B 684 -1 O GLN B 681 N THR B 673 SHEET 4 AA2 6 VAL B 689 VAL B 692 -1 O VAL B 690 N VAL B 682 SHEET 5 AA2 6 ILE B 701 THR B 704 -1 O THR B 704 N VAL B 689 SHEET 6 AA2 6 SER B 710 PHE B 713 -1 O PHE B 713 N ILE B 701 CRYST1 36.711 53.095 41.637 90.00 107.92 90.00 P 1 21 1 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 0.027240 0.000000 0.008809 0.00000 SCALE2 0.000000 0.018834 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025242 0.00000