HEADER SIGNALING PROTEIN 05-APR-19 6RA0 TITLE A UBIQUITIN-LIKE DIMERIZATION DOMAIN CONTROLS PROTEIN KINASE D TITLE 2 ACTIVATION BY TRANS-AUTOPHOSPHORYLATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE DKF-1; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.11.13; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_COMMON: ROUNDWORM; SOURCE 4 ORGANISM_TAXID: 6239; SOURCE 5 GENE: DKF-1, W09C5.5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: STAR KEYWDS UBIQUITIN-LIKE DOMAIN, ZINC FINGER, DAG-BINDING, C1, SIGNALING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.J.ELSNER,T.A.LEONARD REVDAT 4 15-MAY-24 6RA0 1 REMARK REVDAT 3 09-OCT-19 6RA0 1 JRNL REVDAT 2 28-AUG-19 6RA0 1 JRNL REVDAT 1 14-AUG-19 6RA0 0 JRNL AUTH D.J.ELSNER,K.M.SIESS,T.GOSSENREITER,M.HARTL,T.A.LEONARD JRNL TITL A UBIQUITIN-LIKE DOMAIN CONTROLS PROTEIN KINASE D JRNL TITL 2 DIMERIZATION AND ACTIVATION BY TRANS-AUTOPHOSPHORYLATION. JRNL REF J.BIOL.CHEM. V. 294 14422 2019 JRNL REFN ESSN 1083-351X JRNL PMID 31406020 JRNL DOI 10.1074/JBC.RA119.008713 REMARK 2 REMARK 2 RESOLUTION. 2.26 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15_3459 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) : 2.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 6910 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 350 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 41.5200 - 3.2600 1.00 2284 113 0.2011 0.2365 REMARK 3 2 3.2600 - 2.5900 0.99 2160 129 0.3059 0.3679 REMARK 3 3 2.5900 - 2.2600 0.99 2116 108 0.3175 0.3787 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) : 0.304 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 39.617 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 57.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 72.71 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 : 0.009 1115 REMARK 3 ANGLE : 1.071 1503 REMARK 3 CHIRALITY : 0.062 165 REMARK 3 PLANARITY : 0.005 198 REMARK 3 DIHEDRAL : 4.535 680 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): 34.5468 9.7471 -5.5259 REMARK 3 T TENSOR REMARK 3 T11: 0.4810 T22: 0.5007 REMARK 3 T33: 0.5815 T12: 0.0648 REMARK 3 T13: 0.0280 T23: -0.0112 REMARK 3 L TENSOR REMARK 3 L11: 1.4858 L22: 4.2639 REMARK 3 L33: 2.0375 L12: -0.7998 REMARK 3 L13: 0.7072 L23: -1.1204 REMARK 3 S TENSOR REMARK 3 S11: 0.1411 S12: 0.0269 S13: -0.2082 REMARK 3 S21: -0.1961 S22: -0.0955 S23: 0.3826 REMARK 3 S31: -0.2417 S32: -0.2541 S33: -0.0277 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 6RA0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-APR-19. REMARK 100 THE DEPOSITION ID IS D_1292101676. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-15; 21-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : ESRF; ESRF REMARK 200 BEAMLINE : ID29; ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97626; 1.28254 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL; PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F; DECTRIS REMARK 200 PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6939 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.260 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.26 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 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) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD 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 (%): 44.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6.8% PEG8000 18% ETHYLENE GLYCOL 0.1 M REMARK 280 MES, PH 6.5 0.03 M NAF 0.03 M NABR 0.03 M NAI, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 22.70650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.50900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.70650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.50900 REMARK 290 SMTRY3 4 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 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 90.82600 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 REMARK 465 ASP A 2 REMARK 465 GLY A 3 REMARK 465 SER A 4 REMARK 465 GLN A 5 REMARK 465 GLY A 6 REMARK 465 SER A 7 REMARK 465 THR A 8 REMARK 465 ASP A 9 REMARK 465 TYR A 10 REMARK 465 GLY A 11 REMARK 465 ALA A 150 REMARK 465 PRO A 151 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 HIS A 30 147.82 -172.18 REMARK 500 ASN A 50 21.67 38.35 REMARK 500 SER A 65 79.99 -151.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 99 ND1 REMARK 620 2 CYS A 129 SG 114.6 REMARK 620 3 CYS A 132 SG 95.5 119.5 REMARK 620 4 CYS A 148 SG 109.3 110.6 106.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 112 SG REMARK 620 2 CYS A 115 SG 110.5 REMARK 620 3 HIS A 137 ND1 100.9 109.3 REMARK 620 4 CYS A 140 SG 107.7 119.7 107.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 202 DBREF 6RA0 A 1 151 UNP Q9XUJ7 DKF1_CAEEL 1 151 SEQADV 6RA0 GLY A -1 UNP Q9XUJ7 EXPRESSION TAG SEQADV 6RA0 ALA A 0 UNP Q9XUJ7 EXPRESSION TAG SEQRES 1 A 153 GLY ALA MET ASP GLY SER GLN GLY SER THR ASP TYR GLY SEQRES 2 A 153 ASP HIS VAL VAL LEU ARG TYR GLY GLY THR ARG GLU MET SEQRES 3 A 153 VAL PRO LEU ILE ARG HIS GLU GLN MET LEU ASP MET LEU SEQRES 4 A 153 MET GLU ARG ALA ARG GLN ILE VAL GLN GLY PHE GLY ASN SEQRES 5 A 153 LEU ASP THR ARG ASN MET TYR LEU PHE ARG HIS GLU TYR SEQRES 6 A 153 ASN SER PRO THR LEU LEU TYR PRO ILE THR SER ALA SER SEQRES 7 A 153 GLN ILE THR SER GLY SER ILE LEU GLU ILE ILE LEU VAL SEQRES 8 A 153 ASP ARG THR GLU ALA ALA VAL ILE PRO HIS VAL VAL GLU SEQRES 9 A 153 PRO GLU SER TYR MET ARG PRO THR PHE CYS ASP PHE CYS SEQRES 10 A 153 GLY GLU MET LEU THR GLY LEU MET ARG GLN GLY VAL LYS SEQRES 11 A 153 CYS LYS ASN CYS ASN GLY ASN PHE HIS LYS ARG CYS SER SEQRES 12 A 153 ASN ALA ALA ARG ASN ASN CYS GLY ALA PRO HET ZN A 201 1 HET ZN A 202 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 AA1 GLN A 32 ASN A 50 1 19 HELIX 2 AA2 SER A 74 ILE A 78 5 5 HELIX 3 AA3 HIS A 137 SER A 141 5 5 SHEET 1 AA1 5 THR A 21 PRO A 26 0 SHEET 2 AA1 5 HIS A 13 TYR A 18 -1 N TYR A 18 O THR A 21 SHEET 3 AA1 5 ILE A 83 LEU A 88 1 O LEU A 84 N VAL A 15 SHEET 4 AA1 5 MET A 56 GLU A 62 -1 N PHE A 59 O GLU A 85 SHEET 5 AA1 5 SER A 65 PRO A 71 -1 O TYR A 70 N ARG A 60 SHEET 1 AA2 3 VAL A 101 GLU A 104 0 SHEET 2 AA2 3 GLY A 126 CYS A 129 -1 O LYS A 128 N GLU A 102 SHEET 3 AA2 3 ASN A 135 PHE A 136 -1 O PHE A 136 N VAL A 127 LINK ND1 HIS A 99 ZN ZN A 201 1555 1555 2.17 LINK SG CYS A 112 ZN ZN A 202 1555 1555 2.29 LINK SG CYS A 115 ZN ZN A 202 1555 1555 2.35 LINK SG CYS A 129 ZN ZN A 201 1555 1555 2.39 LINK SG CYS A 132 ZN ZN A 201 1555 1555 2.21 LINK ND1 HIS A 137 ZN ZN A 202 1555 1555 2.10 LINK SG CYS A 140 ZN ZN A 202 1555 1555 2.30 LINK SG CYS A 148 ZN ZN A 201 1555 1555 2.49 SITE 1 AC1 4 HIS A 99 CYS A 129 CYS A 132 CYS A 148 SITE 1 AC2 4 CYS A 112 CYS A 115 HIS A 137 CYS A 140 CRYST1 45.413 83.018 37.080 90.00 90.00 90.00 P 21 21 2 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 0.022020 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012046 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026969 0.00000