HEADER TRANSFERASE 24-MAR-15 4YYP TITLE CRYSTAL STRUCTURE OF HUMAN PLK4-PB3 IN COMPLEX WITH STIL-CC COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE PLK4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 884-970; COMPND 5 SYNONYM: POLO-LIKE KINASE 4,PLK-4,SERINE/THREONINE-PROTEIN KINASE 18, COMPND 6 SERINE/THREONINE-PROTEIN KINASE SAK; COMPND 7 EC: 2.7.11.21; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: SCL-INTERRUPTING LOCUS PROTEIN; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: RESIDUES 720-751; COMPND 13 SYNONYM: TAL-1-INTERRUPTING LOCUS PROTEIN; COMPND 14 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: PLK4, SAK, STK18; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PETG-30A; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS POLO-BOX, COMPLEX, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.IMSENG,C.ARQUINT,A.GABRYJONCZYK,R.BOEHM,E.SAUER,S.HILLER,E.A.NIGG, AUTHOR 2 T.MAIER REVDAT 2 10-JAN-24 4YYP 1 REMARK REVDAT 1 29-JUL-15 4YYP 0 JRNL AUTH C.ARQUINT,A.M.GABRYJONCZYK,S.IMSENG,R.BOHM,E.SAUER,S.HILLER, JRNL AUTH 2 E.A.NIGG,T.MAIER JRNL TITL STIL BINDING TO POLO-BOX 3 OF PLK4 REGULATES CENTRIOLE JRNL TITL 2 DUPLICATION. JRNL REF ELIFE V. 4 2015 JRNL REFN ESSN 2050-084X JRNL PMID 26188084 JRNL DOI 10.7554/ELIFE.07888 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.0 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 6409 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.850 REMARK 3 FREE R VALUE TEST SET COUNT : 631 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.72 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 1774 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.3055 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1584 REMARK 3 BIN R VALUE (WORKING SET) : 0.2969 REMARK 3 BIN FREE R VALUE : 0.3790 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.71 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 190 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 943 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 15 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 89.04 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 89.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 27.63370 REMARK 3 B22 (A**2) : -56.76300 REMARK 3 B33 (A**2) : 29.12940 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.504 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.354 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.255 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.889 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.879 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1848 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 3304 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 413 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 29 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 265 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1848 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 125 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 2037 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.15 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.90 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 18.59 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4YYP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000208280. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 - 7.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6428 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 68.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.15000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 2.37000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.900 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: 3P34 REMARK 200 REMARK 200 REMARK: THIN, PLATE-LIKE CRYSTALS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THIN NEEDLES GREW IN PRECIPITANT REMARK 280 SOLUTION CONTAINING 100 MM HEPES, PH 7.0, 20 MM MGCL2 AND 22% REMARK 280 POLY(ACRYLIC ACID SODIUM SALT) 5100. AFTER EXTENSIVE REMARK 280 OPTIMIZATION AND SEEDING PLATE-LIKE CRYSTALS WERE GROWN IN A REMARK 280 DROP CONSISTING OF 50% PLK4-PB3/STIL-CC COMPLEX SOLUTION, 33.3% REMARK 280 PRECIPITANT SOLUTION (100 MM PHOSPHATE/CITRATE PH 4.2, 40% (V/V) REMARK 280 ETHANOL, 5% (W/V) PEG 1000) AND 16.7% OF SEED STOCK SOLUTION., REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 16.72000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 16.72000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 43.28500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 68.16500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 43.28500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 68.16500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 16.72000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 43.28500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 68.16500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 16.72000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 43.28500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 68.16500 REMARK 290 SMTRY3 8 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 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 ASN A 895 61.39 -111.53 REMARK 500 ASN A 941 61.90 -119.06 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 CL A 1001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2N15 RELATED DB: PDB DBREF 4YYP A 884 970 UNP O00444 PLK4_HUMAN 884 970 DBREF 4YYP B 720 751 UNP Q15468 STIL_HUMAN 720 751 SEQRES 1 A 87 SER ALA GLN LEU LEU LYS SER VAL PHE VAL LYS ASN VAL SEQRES 2 A 87 GLY TRP ALA THR GLN LEU THR SER GLY ALA VAL TRP VAL SEQRES 3 A 87 GLN PHE ASN ASP GLY SER GLN LEU VAL VAL GLN ALA GLY SEQRES 4 A 87 VAL SER SER ILE SER TYR THR SER PRO ASN GLY GLN THR SEQRES 5 A 87 THR ARG TYR GLY GLU ASN GLU LYS LEU PRO ASP TYR ILE SEQRES 6 A 87 LYS GLN LYS LEU GLN CYS LEU SER SER ILE LEU LEU MET SEQRES 7 A 87 PHE SER ASN PRO THR PRO ASN PHE HIS SEQRES 1 B 32 PRO ASP ALA TYR ARG PHE LEU THR GLU GLN ASP ARG GLN SEQRES 2 B 32 LEU ARG LEU LEU GLN ALA GLN ILE GLN ARG LEU LEU GLU SEQRES 3 B 32 ALA GLN SER LEU MET PRO HET CL A1001 1 HETNAM CL CHLORIDE ION FORMUL 3 CL CL 1- FORMUL 4 HOH *15(H2 O) HELIX 1 AA1 PRO A 945 LEU A 959 1 15 HELIX 2 AA2 LEU A 960 PHE A 962 5 3 HELIX 3 AA3 ASP B 721 MET B 750 1 30 SHEET 1 AA1 6 LEU A 887 VAL A 893 0 SHEET 2 AA1 6 GLY A 897 LEU A 902 -1 O GLY A 897 N VAL A 893 SHEET 3 AA1 6 ALA A 906 PHE A 911 -1 O GLN A 910 N TRP A 898 SHEET 4 AA1 6 GLN A 916 GLN A 920 -1 O VAL A 919 N VAL A 907 SHEET 5 AA1 6 ILE A 926 THR A 929 -1 O THR A 929 N GLN A 916 SHEET 6 AA1 6 THR A 935 TYR A 938 -1 O THR A 936 N TYR A 928 CISPEP 1 LYS A 894 ASN A 895 0 -4.46 CISPEP 2 MET B 750 PRO B 751 0 3.81 SITE 1 AC1 4 TRP A 898 THR A 900 TRP A 908 GLN A 910 CRYST1 86.570 136.330 33.440 90.00 90.00 90.00 C 2 2 21 8 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 0.011551 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007335 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029904 0.00000