HEADER TRANSFERASE 27-DEC-04 1WVW TITLE CRYSTAL STRUCTURES OF KINASE DOMAIN OF DAP KINASE IN COMPLEX WITH TITLE 2 SMALL MOLECULAR INHIBITORS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEATH-ASSOCIATED PROTEIN KINASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: DAP KINASE 1; COMPND 6 EC: 2.7.1.37; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET31 KEYWDS PROTEIN KINASE, APOPTOSIS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.UEDA,H.OGATA,A.YAMAKAWA,Y.HIGUCHI REVDAT 3 25-OCT-23 1WVW 1 REMARK REVDAT 2 24-FEB-09 1WVW 1 VERSN REVDAT 1 11-APR-06 1WVW 0 JRNL AUTH Y.UEDA,H.OGATA,A.YAMAKAWA,Y.HIGUCHI JRNL TITL CRYSTAL STRUCTURE OF KINASE DOMAIN OF DAP KINASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1036676.070 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.2 REMARK 3 NUMBER OF REFLECTIONS : 15527 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 SET) : 0.232 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1720 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.42 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2565 REMARK 3 BIN R VALUE (WORKING SET) : 0.3132 REMARK 3 BIN FREE R VALUE : 0.3532 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 40 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 : 2231 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.17000 REMARK 3 B22 (A**2) : -3.05000 REMARK 3 B33 (A**2) : -1.12000 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) : 0.37 REMARK 3 ESD FROM SIGMAA (A) : 0.32 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.42 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.37 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.700 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.530 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.550 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.170 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.330 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 24.36 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1WVW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1000024064. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-OCT-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL40B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17268 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.11800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.34600 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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1KOB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CACODYLATE, PEG8000, MAGNESIUM REMARK 280 ACETATE, GLYCEROL, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 283K 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 38.99600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 25.03150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.95450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 25.03150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.99600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 54.95450 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 PRO A 277 REMARK 465 LYS A 278 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 SER A 21 123.19 -170.55 REMARK 500 ARG A 48 13.84 46.02 REMARK 500 GLN A 72 80.93 -160.98 REMARK 500 ASN A 85 -158.77 -136.13 REMARK 500 LYS A 108 -158.64 -45.70 REMARK 500 SER A 110 123.49 -12.00 REMARK 500 ASP A 139 34.64 -146.17 REMARK 500 ASN A 151 51.10 -112.52 REMARK 500 ASP A 161 85.60 56.98 REMARK 500 PHE A 162 32.21 -98.34 REMARK 500 ASN A 172 102.90 60.26 REMARK 500 ASN A 176 147.81 -29.33 REMARK 500 PHE A 178 -169.08 -172.38 REMARK 500 PHE A 236 65.55 -104.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WVX RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH BDB402 REMARK 900 RELATED ID: 1WVY RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH STU DBREF 1WVW A 1 278 UNP P53355 DAPK1_HUMAN 1 278 SEQRES 1 A 278 MET THR VAL PHE ARG GLN GLU ASN VAL ASP ASP TYR TYR SEQRES 2 A 278 ASP THR GLY GLU GLU LEU GLY SER GLY GLN PHE ALA VAL SEQRES 3 A 278 VAL LYS LYS CYS ARG GLU LYS SER THR GLY LEU GLN TYR SEQRES 4 A 278 ALA ALA LYS PHE ILE LYS LYS ARG ARG THR LYS SER SER SEQRES 5 A 278 ARG ARG GLY VAL SER ARG GLU ASP ILE GLU ARG GLU VAL SEQRES 6 A 278 SER ILE LEU LYS GLU ILE GLN HIS PRO ASN VAL ILE THR SEQRES 7 A 278 LEU HIS GLU VAL TYR GLU ASN LYS THR ASP VAL ILE LEU SEQRES 8 A 278 ILE LEU GLU LEU VAL ALA GLY GLY GLU LEU PHE ASP PHE SEQRES 9 A 278 LEU ALA GLU LYS GLU SER LEU THR GLU GLU GLU ALA THR SEQRES 10 A 278 GLU PHE LEU LYS GLN ILE LEU ASN GLY VAL TYR TYR LEU SEQRES 11 A 278 HIS SER LEU GLN ILE ALA HIS PHE ASP LEU LYS PRO GLU SEQRES 12 A 278 ASN ILE MET LEU LEU ASP ARG ASN VAL PRO LYS PRO ARG SEQRES 13 A 278 ILE LYS ILE ILE ASP PHE GLY LEU ALA HIS LYS ILE ASP SEQRES 14 A 278 PHE GLY ASN GLU PHE LYS ASN ILE PHE GLY THR PRO GLU SEQRES 15 A 278 PHE VAL ALA PRO GLU ILE VAL ASN TYR GLU PRO LEU GLY SEQRES 16 A 278 LEU GLU ALA ASP MET TRP SER ILE GLY VAL ILE THR TYR SEQRES 17 A 278 ILE LEU LEU SER GLY ALA SER PRO PHE LEU GLY ASP THR SEQRES 18 A 278 LYS GLN GLU THR LEU ALA ASN VAL SER ALA VAL ASN TYR SEQRES 19 A 278 GLU PHE GLU ASP GLU TYR PHE SER ASN THR SER ALA LEU SEQRES 20 A 278 ALA LYS ASP PHE ILE ARG ARG LEU LEU VAL LYS ASP PRO SEQRES 21 A 278 LYS LYS ARG MET THR ILE GLN ASP SER LEU GLN HIS PRO SEQRES 22 A 278 TRP ILE LYS PRO LYS HELIX 1 1 ASN A 8 ASP A 11 5 4 HELIX 2 2 GLU A 59 ILE A 71 1 13 HELIX 3 3 GLU A 100 ALA A 106 1 7 HELIX 4 4 THR A 112 LEU A 133 1 22 HELIX 5 5 LYS A 141 GLU A 143 5 3 HELIX 6 6 THR A 180 VAL A 184 5 5 HELIX 7 7 ALA A 185 ASN A 190 1 6 HELIX 8 8 LEU A 196 GLY A 213 1 18 HELIX 9 9 THR A 221 ALA A 231 1 11 HELIX 10 10 GLU A 237 SER A 242 1 6 HELIX 11 11 SER A 245 ARG A 254 1 10 HELIX 12 12 ASP A 259 ARG A 263 5 5 HELIX 13 13 THR A 265 GLN A 271 1 7 SHEET 1 A 5 TYR A 13 SER A 21 0 SHEET 2 A 5 ALA A 25 GLU A 32 -1 O LYS A 29 N GLU A 17 SHEET 3 A 5 GLN A 38 LYS A 45 -1 O ALA A 41 N LYS A 28 SHEET 4 A 5 ASP A 88 GLU A 94 -1 O LEU A 93 N ALA A 40 SHEET 5 A 5 LEU A 79 GLU A 84 -1 N GLU A 81 O ILE A 92 SHEET 1 B 2 ILE A 135 ALA A 136 0 SHEET 2 B 2 HIS A 166 LYS A 167 -1 O HIS A 166 N ALA A 136 SHEET 1 C 2 ILE A 145 LEU A 147 0 SHEET 2 C 2 ILE A 157 ILE A 159 -1 O LYS A 158 N MET A 146 CRYST1 77.992 109.909 50.063 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 0.012822 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009098 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019975 0.00000