HEADER STRUCTURAL PROTEIN 13-JUL-16 5LHX TITLE PB3 DOMAIN OF DROSOPHILA MELANOGASTER PLK4 (SAK) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE PLK4; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 657-745; 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 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 B; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 37762; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: B834 KEYWDS POLO BOX DOMAIN, CENTRIOLE, TRANSFERASE, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.A.COTTEE,S.M.LEA REVDAT 5 10-JAN-24 5LHX 1 REMARK REVDAT 4 10-MAY-17 5LHX 1 JRNL REVDAT 3 29-MAR-17 5LHX 1 JRNL REVDAT 2 08-MAR-17 5LHX 1 JRNL REVDAT 1 01-MAR-17 5LHX 0 JRNL AUTH M.A.COTTEE,S.JOHNSON,J.W.RAFF,S.M.LEA JRNL TITL A KEY CENTRIOLE ASSEMBLY INTERACTION INTERFACE BETWEEN HUMAN JRNL TITL 2 PLK4 AND STIL APPEARS TO NOT BE CONSERVED IN FLIES. JRNL REF BIOL OPEN V. 6 381 2017 JRNL REFN ESSN 2046-6390 JRNL PMID 28202467 JRNL DOI 10.1242/BIO.024661 REMARK 2 REMARK 2 RESOLUTION. 1.53 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 22153 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1092 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 40.6555 - 3.0597 0.97 2669 134 0.1601 0.1876 REMARK 3 2 3.0597 - 2.4286 0.97 2616 151 0.1883 0.2205 REMARK 3 3 2.4286 - 2.1217 0.98 2637 137 0.1554 0.2134 REMARK 3 4 2.1217 - 1.9277 0.98 2674 122 0.1349 0.2067 REMARK 3 5 1.9277 - 1.7895 0.98 2633 135 0.1425 0.2009 REMARK 3 6 1.7895 - 1.6840 0.98 2635 136 0.1711 0.2698 REMARK 3 7 1.6840 - 1.5997 0.98 2635 131 0.2280 0.2753 REMARK 3 8 1.5997 - 1.5300 0.96 2562 146 0.3161 0.3758 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.740 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 : 0.010 1322 REMARK 3 ANGLE : 1.014 1799 REMARK 3 CHIRALITY : 0.065 209 REMARK 3 PLANARITY : 0.008 236 REMARK 3 DIHEDRAL : 11.043 794 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 5LHX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1200000760. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22170 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 REMARK 200 RESOLUTION RANGE LOW (A) : 40.641 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.89100 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: 4YYP REMARK 200 REMARK 200 REMARK: LARGE TEARDROPS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 150 NL PROTEIN SOLUTION (40.0 MG/ML REMARK 280 PROTEIN IN IN 20 MM TRIS PH 7.5, 150 MM NACL, 2 MM DTT) AND 50 REMARK 280 NL MOTHER LIQUOR (1.5 M AMMONIUM SULPHATE, 2% V/V PEG400, 100 MM REMARK 280 NA HEPES PH 7.5), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K 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 26.07000 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 PRO A 654 REMARK 465 MET A 655 REMARK 465 GLY A 656 REMARK 465 GLN A 657 REMARK 465 SER A 745 REMARK 465 GLY B 653 REMARK 465 PRO B 654 REMARK 465 MET B 655 REMARK 465 GLY B 656 REMARK 465 GLN B 657 REMARK 465 ASN B 658 REMARK 465 ILE B 659 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 -5.60 75.95 REMARK 500 GLU B 668 -22.16 77.67 REMARK 500 ILE B 669 -60.68 -104.51 REMARK 500 REMARK 500 REMARK: NULL DBREF 5LHX A 657 745 UNP O97143 PLK4_DROME 657 745 DBREF 5LHX B 657 745 UNP O97143 PLK4_DROME 657 745 SEQADV 5LHX GLY A 653 UNP O97143 EXPRESSION TAG SEQADV 5LHX PRO A 654 UNP O97143 EXPRESSION TAG SEQADV 5LHX MET A 655 UNP O97143 EXPRESSION TAG SEQADV 5LHX GLY A 656 UNP O97143 EXPRESSION TAG SEQADV 5LHX GLY B 653 UNP O97143 EXPRESSION TAG SEQADV 5LHX PRO B 654 UNP O97143 EXPRESSION TAG SEQADV 5LHX MET B 655 UNP O97143 EXPRESSION TAG SEQADV 5LHX GLY B 656 UNP O97143 EXPRESSION TAG SEQRES 1 A 93 GLY PRO MET GLY 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 PRO MET GLY 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 *35(H2 O) HELIX 1 AA1 PRO A 694 GLY A 698 5 5 HELIX 2 AA2 PRO A 722 GLY A 728 1 7 HELIX 3 AA3 GLN A 729 THR A 739 1 11 HELIX 4 AA4 PRO B 720 GLY B 728 1 9 HELIX 5 AA5 GLN B 729 ALA B 740 1 12 SHEET 1 AA1 6 PRO A 660 VAL A 666 0 SHEET 2 AA1 6 GLY A 670 LEU A 675 -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 692 N VAL A 680 SHEET 5 AA1 6 ILE A 701 THR A 704 -1 O THR A 704 N VAL A 689 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 CISPEP 1 PHE A 721 PRO A 722 0 -0.64 CRYST1 35.870 52.140 42.530 90.00 107.14 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 0.027878 0.000000 0.008598 0.00000 SCALE2 0.000000 0.019179 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024606 0.00000