HEADER TRANSFERASE 10-JUN-15 5AUZ TITLE CRYSTAL STRUCTURE OF DAPK1 IN COMPLEX WITH GENISTEIN. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEATH-ASSOCIATED PROTEIN KINASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-285; COMPND 5 SYNONYM: DAP KINASE 1; COMPND 6 EC: 2.7.11.1; COMPND 7 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: DAPK1, DAPK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DEATH-ASSOCIATED PROTEIN KINASE 1, SERINE/THREONINE PROTEIN KINASE, KEYWDS 2 NATURAL FLAVONOID, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR T.YOKOYAMA,M.MIZUGUCHI REVDAT 3 20-MAR-24 5AUZ 1 REMARK REVDAT 2 19-FEB-20 5AUZ 1 SOURCE KEYWDS JRNL REMARK REVDAT 1 07-OCT-15 5AUZ 0 JRNL AUTH T.YOKOYAMA,Y.KOSAKA,M.MIZUGUCHI JRNL TITL STRUCTURAL INSIGHT INTO THE INTERACTIONS BETWEEN JRNL TITL 2 DEATH-ASSOCIATED PROTEIN KINASE 1 AND NATURAL FLAVONOIDS. JRNL REF J.MED.CHEM. V. 58 7400 2015 JRNL REFN ISSN 0022-2623 JRNL PMID 26322379 JRNL DOI 10.1021/ACS.JMEDCHEM.5B00893 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.430 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 34618 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1743 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 34.4517 - 3.6572 0.98 2898 151 0.1742 0.1982 REMARK 3 2 3.6572 - 2.9033 0.99 2790 159 0.1674 0.1881 REMARK 3 3 2.9033 - 2.5364 0.99 2782 143 0.1784 0.1918 REMARK 3 4 2.5364 - 2.3046 0.99 2727 156 0.1678 0.2003 REMARK 3 5 2.3046 - 2.1394 0.99 2752 126 0.1564 0.1976 REMARK 3 6 2.1394 - 2.0133 0.99 2709 155 0.1564 0.1996 REMARK 3 7 2.0133 - 1.9125 0.99 2749 153 0.1675 0.2064 REMARK 3 8 1.9125 - 1.8292 0.99 2732 115 0.1777 0.2351 REMARK 3 9 1.8292 - 1.7588 0.99 2688 158 0.1928 0.2388 REMARK 3 10 1.7588 - 1.6981 0.99 2717 128 0.2165 0.2355 REMARK 3 11 1.6981 - 1.6450 0.99 2667 164 0.2257 0.2401 REMARK 3 12 1.6450 - 1.5980 0.97 2664 135 0.2569 0.3018 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.170 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 : 0.007 2287 REMARK 3 ANGLE : 1.074 3091 REMARK 3 CHIRALITY : 0.076 341 REMARK 3 PLANARITY : 0.005 397 REMARK 3 DIHEDRAL : 14.682 870 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 5AUZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1300000032. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34651 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 34.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL 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) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 M AMMONIUM SULFATE, 0.1 M MES, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 23.36000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.32000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.15900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.32000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.36000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.15900 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: 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 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 MET A 1 REMARK 465 LYS A 108 REMARK 465 GLU A 109 REMARK 465 LYS A 278 REMARK 465 ASP A 279 REMARK 465 THR A 280 REMARK 465 GLN A 281 REMARK 465 GLN A 282 REMARK 465 ALA A 283 REMARK 465 LEU A 284 REMARK 465 SER A 285 REMARK 465 LEU A 286 REMARK 465 GLU A 287 REMARK 465 HIS A 288 REMARK 465 HIS A 289 REMARK 465 HIS A 290 REMARK 465 HIS A 291 REMARK 465 HIS A 292 REMARK 465 HIS A 293 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 ASP A 139 39.44 -145.69 REMARK 500 ASN A 151 49.38 -102.38 REMARK 500 ASP A 161 80.65 68.96 REMARK 500 ILE A 168 71.54 -112.61 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 GEN A 400 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5AUT RELATED DB: PDB REMARK 900 RELATED ID: 5AUU RELATED DB: PDB REMARK 900 RELATED ID: 5AUV RELATED DB: PDB REMARK 900 RELATED ID: 5AUW RELATED DB: PDB REMARK 900 RELATED ID: 5AUX RELATED DB: PDB REMARK 900 RELATED ID: 5AUY RELATED DB: PDB REMARK 900 RELATED ID: 5AV0 RELATED DB: PDB REMARK 900 RELATED ID: 5AV1 RELATED DB: PDB REMARK 900 RELATED ID: 5AV2 RELATED DB: PDB REMARK 900 RELATED ID: 5AV3 RELATED DB: PDB REMARK 900 RELATED ID: 5AV4 RELATED DB: PDB DBREF 5AUZ A 1 285 UNP P53355 DAPK1_HUMAN 1 285 SEQADV 5AUZ LEU A 286 UNP P53355 EXPRESSION TAG SEQADV 5AUZ GLU A 287 UNP P53355 EXPRESSION TAG SEQADV 5AUZ HIS A 288 UNP P53355 EXPRESSION TAG SEQADV 5AUZ HIS A 289 UNP P53355 EXPRESSION TAG SEQADV 5AUZ HIS A 290 UNP P53355 EXPRESSION TAG SEQADV 5AUZ HIS A 291 UNP P53355 EXPRESSION TAG SEQADV 5AUZ HIS A 292 UNP P53355 EXPRESSION TAG SEQADV 5AUZ HIS A 293 UNP P53355 EXPRESSION TAG SEQRES 1 A 293 MET THR VAL PHE ARG GLN GLU ASN VAL ASP ASP TYR TYR SEQRES 2 A 293 ASP THR GLY GLU GLU LEU GLY SER GLY GLN PHE ALA VAL SEQRES 3 A 293 VAL LYS LYS CYS ARG GLU LYS SER THR GLY LEU GLN TYR SEQRES 4 A 293 ALA ALA LYS PHE ILE LYS LYS ARG ARG THR LYS SER SER SEQRES 5 A 293 ARG ARG GLY VAL SER ARG GLU ASP ILE GLU ARG GLU VAL SEQRES 6 A 293 SER ILE LEU LYS GLU ILE GLN HIS PRO ASN VAL ILE THR SEQRES 7 A 293 LEU HIS GLU VAL TYR GLU ASN LYS THR ASP VAL ILE LEU SEQRES 8 A 293 ILE LEU GLU LEU VAL ALA GLY GLY GLU LEU PHE ASP PHE SEQRES 9 A 293 LEU ALA GLU LYS GLU SER LEU THR GLU GLU GLU ALA THR SEQRES 10 A 293 GLU PHE LEU LYS GLN ILE LEU ASN GLY VAL TYR TYR LEU SEQRES 11 A 293 HIS SER LEU GLN ILE ALA HIS PHE ASP LEU LYS PRO GLU SEQRES 12 A 293 ASN ILE MET LEU LEU ASP ARG ASN VAL PRO LYS PRO ARG SEQRES 13 A 293 ILE LYS ILE ILE ASP PHE GLY LEU ALA HIS LYS ILE ASP SEQRES 14 A 293 PHE GLY ASN GLU PHE LYS ASN ILE PHE GLY THR PRO GLU SEQRES 15 A 293 PHE VAL ALA PRO GLU ILE VAL ASN TYR GLU PRO LEU GLY SEQRES 16 A 293 LEU GLU ALA ASP MET TRP SER ILE GLY VAL ILE THR TYR SEQRES 17 A 293 ILE LEU LEU SER GLY ALA SER PRO PHE LEU GLY ASP THR SEQRES 18 A 293 LYS GLN GLU THR LEU ALA ASN VAL SER ALA VAL ASN TYR SEQRES 19 A 293 GLU PHE GLU ASP GLU TYR PHE SER ASN THR SER ALA LEU SEQRES 20 A 293 ALA LYS ASP PHE ILE ARG ARG LEU LEU VAL LYS ASP PRO SEQRES 21 A 293 LYS LYS ARG MET THR ILE GLN ASP SER LEU GLN HIS PRO SEQRES 22 A 293 TRP ILE LYS PRO LYS ASP THR GLN GLN ALA LEU SER LEU SEQRES 23 A 293 GLU HIS HIS HIS HIS HIS HIS HET GEN A 400 20 HETNAM GEN GENISTEIN HETSYN GEN 5,7-DIHYDROXY-3-(4-HYDROXYPHENYL)-4H-1-BENZOPYRAN-4- HETSYN 2 GEN ONE; 4',5,7-TRIHYDROXYISOFLAVONE; PRUNETOL; GENISTEOL FORMUL 2 GEN C15 H10 O5 FORMUL 3 HOH *246(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 GLU A 107 1 8 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 ALA A 185 ASN A 190 1 6 HELIX 7 AA7 LEU A 196 GLY A 213 1 18 HELIX 8 AA8 THR A 221 VAL A 232 1 12 HELIX 9 AA9 GLU A 237 SER A 242 1 6 HELIX 10 AB1 SER A 245 ARG A 254 1 10 HELIX 11 AB2 THR A 265 HIS A 272 1 8 SHEET 1 AA1 5 TYR A 13 SER A 21 0 SHEET 2 AA1 5 ALA A 25 GLU A 32 -1 O LYS A 29 N GLU A 17 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 VAL A 89 N ILE A 44 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 SITE 1 AC1 10 VAL A 27 ALA A 40 LYS A 42 GLU A 94 SITE 2 AC1 10 LEU A 95 VAL A 96 ILE A 160 ASP A 161 SITE 3 AC1 10 HOH A 533 HOH A 559 CRYST1 46.720 62.318 88.640 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 0.021404 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016047 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011282 0.00000