HEADER SIGNALING PROTEIN 12-JAN-18 6FHA TITLE DEATH-ASSOCIATED PROTEIN KINASE 1 (DAPK1) CATALYTIC AND AUTO- TITLE 2 REGULATORY DOMAINS WITH S289A AND S308A MUTATIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEATH-ASSOCIATED PROTEIN KINASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DAP KINASE 1; COMPND 5 EC: 2.7.11.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DAPK1, DAPK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KINASE, APOPTOSIS, AUTOPHAGY, CAMK, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.-S.HUART,M.WILMANNS REVDAT 2 17-JAN-24 6FHA 1 REMARK REVDAT 1 30-JAN-19 6FHA 0 JRNL AUTH A.-S.HUART,B.SIMON,J.LUBNER,H.D.T.MERTENS,K.TEMMERMAN, JRNL AUTH 2 J.-E.HOFFMANN,D.I.SVERGUN,D.SCHWARTZ,C.SCHULTZ,M.WILMANNS JRNL TITL MOLECULAR MECHANISMS BEHIND DAPK REGULATION: HOW JRNL TITL 2 PHOSPHORYLATION SWITCHES WORK JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9-1692 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 15161 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.740 REMARK 3 FREE R VALUE TEST SET COUNT : 719 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 39.9491 - 3.9322 0.97 2991 140 0.1849 0.2317 REMARK 3 2 3.9322 - 3.1215 0.98 2890 135 0.1864 0.2632 REMARK 3 3 3.1215 - 2.7270 0.99 2863 148 0.2131 0.2854 REMARK 3 4 2.7270 - 2.4777 0.99 2848 156 0.2401 0.3175 REMARK 3 5 2.4777 - 2.3001 0.99 2850 140 0.2642 0.3355 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.580 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.98 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 : 0.009 2474 REMARK 3 ANGLE : 1.194 3336 REMARK 3 CHIRALITY : 0.045 368 REMARK 3 PLANARITY : 0.005 431 REMARK 3 DIHEDRAL : 14.712 942 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 6FHA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1200007137. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P14 (MX2) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : TOROIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 7.0.021 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25549 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.878 REMARK 200 RESOLUTION RANGE LOW (A) : 39.943 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.4 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.13400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 36.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.70500 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 PHENIX 1.9-1692 REMARK 200 STARTING MODEL: 4B4L REMARK 200 REMARK 200 REMARK: CUBOID REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG 4000, 0.2M AMMONIUM SULFATE, REMARK 280 0.1M SODIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 292.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 23.49650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.75550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.91000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.75550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.49650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.91000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 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 -2 REMARK 465 PRO A -1 REMARK 465 MET A 0 REMARK 465 ALA A 1 REMARK 465 THR A 2 REMARK 465 VAL A 3 REMARK 465 LYS A 303 REMARK 465 LYS A 304 REMARK 465 TRP A 305 REMARK 465 LYS A 306 REMARK 465 GLN A 307 REMARK 465 ALA A 308 REMARK 465 VAL A 309 REMARK 465 ARG A 310 REMARK 465 LEU A 311 REMARK 465 ILE A 312 REMARK 465 SER A 313 REMARK 465 LEU A 314 REMARK 465 CYS A 315 REMARK 465 GLN A 316 REMARK 465 ARG A 317 REMARK 465 LEU A 318 REMARK 465 SER A 319 REMARK 465 ARG A 320 REMARK 465 SER A 321 REMARK 465 PHE A 322 REMARK 465 LEU A 323 REMARK 465 SER A 324 REMARK 465 ARG A 325 REMARK 465 SER A 326 REMARK 465 ASN A 327 REMARK 465 MET A 328 REMARK 465 SER A 329 REMARK 465 VAL A 330 REMARK 465 ALA A 331 REMARK 465 ARG A 332 REMARK 465 SER A 333 REMARK 465 ASP A 334 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLU A 70 NZ LYS A 167 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 48 -51.04 81.07 REMARK 500 ASN A 85 -159.50 -121.30 REMARK 500 ASP A 139 29.23 -142.19 REMARK 500 ASP A 161 88.10 59.19 REMARK 500 ASN A 176 -90.24 -16.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6FH9 RELATED DB: PDB REMARK 900 OTHER MUTANT DBREF 6FHA A 2 334 UNP P53355 DAPK1_HUMAN 2 334 SEQADV 6FHA GLY A -2 UNP P53355 EXPRESSION TAG SEQADV 6FHA PRO A -1 UNP P53355 EXPRESSION TAG SEQADV 6FHA MET A 0 UNP P53355 EXPRESSION TAG SEQADV 6FHA ALA A 1 UNP P53355 EXPRESSION TAG SEQADV 6FHA ALA A 289 UNP P53355 SER 289 ENGINEERED MUTATION SEQADV 6FHA ALA A 308 UNP P53355 SER 308 ENGINEERED MUTATION SEQRES 1 A 337 GLY PRO MET ALA THR VAL PHE ARG GLN GLU ASN VAL ASP SEQRES 2 A 337 ASP TYR TYR ASP THR GLY GLU GLU LEU GLY SER GLY GLN SEQRES 3 A 337 PHE ALA VAL VAL LYS LYS CYS ARG GLU LYS SER THR GLY SEQRES 4 A 337 LEU GLN TYR ALA ALA LYS PHE ILE LYS LYS ARG ARG THR SEQRES 5 A 337 LYS SER SER ARG ARG GLY VAL SER ARG GLU ASP ILE GLU SEQRES 6 A 337 ARG GLU VAL SER ILE LEU LYS GLU ILE GLN HIS PRO ASN SEQRES 7 A 337 VAL ILE THR LEU HIS GLU VAL TYR GLU ASN LYS THR ASP SEQRES 8 A 337 VAL ILE LEU ILE LEU GLU LEU VAL ALA GLY GLY GLU LEU SEQRES 9 A 337 PHE ASP PHE LEU ALA GLU LYS GLU SER LEU THR GLU GLU SEQRES 10 A 337 GLU ALA THR GLU PHE LEU LYS GLN ILE LEU ASN GLY VAL SEQRES 11 A 337 TYR TYR LEU HIS SER LEU GLN ILE ALA HIS PHE ASP LEU SEQRES 12 A 337 LYS PRO GLU ASN ILE MET LEU LEU ASP ARG ASN VAL PRO SEQRES 13 A 337 LYS PRO ARG ILE LYS ILE ILE ASP PHE GLY LEU ALA HIS SEQRES 14 A 337 LYS ILE ASP PHE GLY ASN GLU PHE LYS ASN ILE PHE GLY SEQRES 15 A 337 THR PRO GLU PHE VAL ALA PRO GLU ILE VAL ASN TYR GLU SEQRES 16 A 337 PRO LEU GLY LEU GLU ALA ASP MET TRP SER ILE GLY VAL SEQRES 17 A 337 ILE THR TYR ILE LEU LEU SER GLY ALA SER PRO PHE LEU SEQRES 18 A 337 GLY ASP THR LYS GLN GLU THR LEU ALA ASN VAL SER ALA SEQRES 19 A 337 VAL ASN TYR GLU PHE GLU ASP GLU TYR PHE SER ASN THR SEQRES 20 A 337 SER ALA LEU ALA LYS ASP PHE ILE ARG ARG LEU LEU VAL SEQRES 21 A 337 LYS ASP PRO LYS LYS ARG MET THR ILE GLN ASP SER LEU SEQRES 22 A 337 GLN HIS PRO TRP ILE LYS PRO LYS ASP THR GLN GLN ALA SEQRES 23 A 337 LEU SER ARG LYS ALA ALA ALA VAL ASN MET GLU LYS PHE SEQRES 24 A 337 LYS LYS PHE ALA ALA ARG LYS LYS TRP LYS GLN ALA VAL SEQRES 25 A 337 ARG LEU ILE SER LEU CYS GLN ARG LEU SER ARG SER PHE SEQRES 26 A 337 LEU SER ARG SER ASN MET SER VAL ALA ARG SER ASP FORMUL 2 HOH *54(H2 O) HELIX 1 AA1 ASN A 8 ASP A 11 5 4 HELIX 2 AA2 SER A 57 ILE A 71 1 15 HELIX 3 AA3 GLU A 100 ALA A 106 1 7 HELIX 4 AA4 THR A 112 LEU A 133 1 22 HELIX 5 AA5 LYS A 141 GLU A 143 5 3 HELIX 6 AA6 THR A 180 VAL A 184 5 5 HELIX 7 AA7 ALA A 185 ASN A 190 1 6 HELIX 8 AA8 LEU A 196 GLY A 213 1 18 HELIX 9 AA9 THR A 221 VAL A 232 1 12 HELIX 10 AB1 GLU A 237 SER A 242 1 6 HELIX 11 AB2 SER A 245 ARG A 254 1 10 HELIX 12 AB3 ASP A 259 ARG A 263 5 5 HELIX 13 AB4 THR A 265 HIS A 272 1 8 HELIX 14 AB5 ASP A 279 ALA A 289 1 11 HELIX 15 AB6 ASN A 292 ALA A 301 1 10 SHEET 1 AA1 5 TYR A 13 SER A 21 0 SHEET 2 AA1 5 ALA A 25 GLU A 32 -1 O VAL A 27 N LEU A 19 SHEET 3 AA1 5 GLN A 38 LYS A 45 -1 O ALA A 41 N LYS A 28 SHEET 4 AA1 5 ASP A 88 GLU A 94 -1 O LEU A 93 N ALA A 40 SHEET 5 AA1 5 LEU A 79 GLU A 84 -1 N TYR A 83 O ILE A 90 SHEET 1 AA2 2 ILE A 135 ALA A 136 0 SHEET 2 AA2 2 HIS A 166 LYS A 167 -1 O HIS A 166 N ALA A 136 SHEET 1 AA3 2 ILE A 145 LEU A 147 0 SHEET 2 AA3 2 ILE A 157 ILE A 159 -1 O LYS A 158 N MET A 146 CRYST1 46.993 75.820 93.511 90.00 90.00 90.00 P 21 21 21 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 0.021280 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013189 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010694 0.00000