HEADER TRANSFERASE 28-APR-14 4PF4 TITLE 1.1A X-RAY STRUCTURE OF THE APO CATALYTIC DOMAIN OF DEATH-ASSOCIATED TITLE 2 PROTEIN KINASE 1, AA 1-277 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 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 BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNEA-VHISGST KEYWDS TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.TEMMERMAN,B.SIMON,M.WILMANNS REVDAT 4 20-DEC-23 4PF4 1 REMARK LINK REVDAT 3 10-DEC-14 4PF4 1 REVDAT 2 16-JUL-14 4PF4 1 TITLE JRNL REVDAT 1 14-MAY-14 4PF4 0 JRNL AUTH K.TEMMERMAN,B.SIMON,M.WILMANNS JRNL TITL 1.1A X-RAY STRUCTURE OF THE APO CATALYTIC DOMAIN OF JRNL TITL 2 DEATH-ASSOCIATED PROTEIN KINASE 1, AA 1-277 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.13 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 95914 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 + TEST SET) : 0.118 REMARK 3 R VALUE (WORKING SET) : 0.117 REMARK 3 FREE R VALUE : 0.150 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4805 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.13 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6304 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.09 REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE SET COUNT : 319 REMARK 3 BIN FREE R VALUE : 0.3140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2232 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 59 REMARK 3 SOLVENT ATOMS : 489 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.09000 REMARK 3 B22 (A**2) : 0.61000 REMARK 3 B33 (A**2) : 0.49000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.028 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.031 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.021 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.024 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.985 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.978 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2470 ; 0.024 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2412 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3350 ; 2.184 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5511 ; 2.168 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 307 ; 6.164 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;36.204 ;24.783 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 447 ;12.907 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;21.611 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 370 ; 0.163 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2793 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 549 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 4882 ; 6.955 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 70 ;36.855 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 5252 ;17.943 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4PF4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000201244. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.973 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS, XSCALE REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 96009 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.129 REMARK 200 RESOLUTION RANGE LOW (A) : 50.758 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) : 0.07600 REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.13 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.70900 REMARK 200 R SYM FOR SHELL (I) : 0.70900 REMARK 200 FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 11.0.05 REMARK 200 STARTING MODEL: 2W4J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, PH=7, 2M AMMONIUM REMARK 280 SULFATE, PH 7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K 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 23.25800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.18750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.00250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.18750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.25800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.00250 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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -75.0 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 48 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 50 CG CD CE NZ REMARK 470 ARG A 53 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 107 CG CD OE1 OE2 REMARK 470 GLU A 109 CG CD OE1 OE2 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 C SER A 269 H LEU A 270 0.46 REMARK 500 C SER A 269 H LEU A 270 0.47 REMARK 500 C ARG A 150 H ASN A 151 0.49 REMARK 500 C ARG A 150 H ASN A 151 0.52 REMARK 500 O HOH A 831 O HOH A 870 1.01 REMARK 500 HO3 GOL A 311 O HOH A 403 1.16 REMARK 500 O HOH A 446 O HOH A 613 1.22 REMARK 500 O HOH A 486 O HOH A 582 1.41 REMARK 500 O SER A 269 H LEU A 270 1.45 REMARK 500 O SER A 269 H LEU A 270 1.48 REMARK 500 HZ3 LYS A 158 O HOH A 402 1.48 REMARK 500 O HOH A 577 O HOH A 770 1.49 REMARK 500 O ARG A 150 H ASN A 151 1.50 REMARK 500 O ARG A 150 H ASN A 151 1.52 REMARK 500 OE1 GLU A 173 O HOH A 401 1.53 REMARK 500 HE3 MET A 146 O HOH A 886 1.53 REMARK 500 O HOH A 437 O HOH A 442 1.58 REMARK 500 HH21 ARG A 150 O HOH A 787 1.60 REMARK 500 O HOH A 506 O HOH A 554 1.62 REMARK 500 O HOH A 741 O HOH A 846 1.65 REMARK 500 O HOH A 725 O HOH A 874 1.66 REMARK 500 O HOH A 544 O HOH A 569 1.67 REMARK 500 O HOH A 613 O HOH A 620 1.70 REMARK 500 O HOH A 818 O HOH A 873 1.71 REMARK 500 O HOH A 589 O HOH A 600 1.79 REMARK 500 O HOH A 817 O HOH A 833 1.83 REMARK 500 NZ LYS A 158 O HOH A 402 1.84 REMARK 500 O HOH A 527 O HOH A 753 1.84 REMARK 500 O HOH A 675 O HOH A 868 1.86 REMARK 500 CE MET A 146 O HOH A 886 1.87 REMARK 500 O HOH A 777 O HOH A 836 1.88 REMARK 500 O HOH A 874 O HOH A 882 1.89 REMARK 500 O3 GOL A 311 O HOH A 403 1.91 REMARK 500 O HOH A 609 O HOH A 803 1.95 REMARK 500 O HOH A 413 O HOH A 591 1.97 REMARK 500 OG SER A 110 O HOH A 702 1.97 REMARK 500 O HOH A 529 O HOH A 604 2.00 REMARK 500 O HOH A 800 O HOH A 886 2.01 REMARK 500 OH TYR A 83 O HOH A 404 2.04 REMARK 500 O HOH A 727 O HOH A 838 2.05 REMARK 500 O HOH A 544 O HOH A 823 2.07 REMARK 500 O HOH A 488 O HOH A 618 2.09 REMARK 500 O HOH A 412 O HOH A 636 2.09 REMARK 500 C3 GOL A 311 O HOH A 404 2.10 REMARK 500 O HOH A 614 O HOH A 626 2.11 REMARK 500 OD1 ASN A 190 O HOH A 405 2.14 REMARK 500 O HOH A 763 O HOH A 838 2.16 REMARK 500 O HOH A 834 O HOH A 871 2.17 REMARK 500 O HOH A 659 O HOH A 836 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 407 O HOH A 480 2455 1.41 REMARK 500 O HOH A 526 O HOH A 586 4455 1.54 REMARK 500 O HOH A 583 O HOH A 634 4555 1.68 REMARK 500 O HOH A 506 O HOH A 550 2454 1.69 REMARK 500 O HOH A 427 O HOH A 546 4455 1.80 REMARK 500 O HOH A 413 O HOH A 485 3455 2.03 REMARK 500 O HOH A 418 O HOH A 500 4555 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 32 CD GLU A 32 OE2 -0.088 REMARK 500 GLU A 114 CD GLU A 114 OE1 -0.077 REMARK 500 TYR A 128 CE1 TYR A 128 CZ -0.103 REMARK 500 GLU A 173 CG GLU A 173 CD 0.170 REMARK 500 GLU A 173 CD GLU A 173 OE2 -0.088 REMARK 500 GLU A 173 CD GLU A 173 OE2 0.163 REMARK 500 GLU A 224 CD GLU A 224 OE1 0.091 REMARK 500 GLU A 224 CD GLU A 224 OE2 -0.085 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLN A 23 O - C - N ANGL. DEV. = -13.4 DEGREES REMARK 500 GLU A 32 OE1 - CD - OE2 ANGL. DEV. = -9.4 DEGREES REMARK 500 ARG A 47 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 54 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 LYS A 86 CD - CE - NZ ANGL. DEV. = 15.2 DEGREES REMARK 500 LEU A 91 CB - CG - CD1 ANGL. DEV. = 14.6 DEGREES REMARK 500 GLU A 143 OE1 - CD - OE2 ANGL. DEV. = -7.5 DEGREES REMARK 500 GLU A 143 CG - CD - OE2 ANGL. DEV. = 16.9 DEGREES REMARK 500 GLU A 173 CG - CD - OE2 ANGL. DEV. = 12.0 DEGREES REMARK 500 ARG A 253 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 253 NE - CZ - NH2 ANGL. DEV. = 5.1 DEGREES 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 ASP A 139 37.59 -145.33 REMARK 500 ASP A 161 80.66 63.06 REMARK 500 ILE A 168 68.84 -117.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 PHE A 174 16.89 REMARK 500 PHE A 174 16.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 780 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH A 808 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A 864 DISTANCE = 7.38 ANGSTROMS 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 NA A 305 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 32 OE1 REMARK 620 2 TYR A 39 OH 101.3 REMARK 620 3 SER A 132 OG 109.5 34.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 312 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 72 OE1 REMARK 620 2 ASP A 169 O 74.3 REMARK 620 3 HOH A 402 O 112.7 87.9 REMARK 620 4 HOH A 497 O 140.4 134.7 55.5 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 SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 311 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 312 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 313 DBREF 4PF4 A 1 277 UNP P53355 DAPK1_HUMAN 1 277 SEQADV 4PF4 HIS A 0 UNP P53355 EXPRESSION TAG SEQRES 1 A 278 HIS MET THR VAL PHE ARG GLN GLU ASN VAL ASP ASP TYR SEQRES 2 A 278 TYR ASP THR GLY GLU GLU LEU GLY SER GLY GLN PHE ALA SEQRES 3 A 278 VAL VAL LYS LYS CYS ARG GLU LYS SER THR GLY LEU GLN SEQRES 4 A 278 TYR ALA ALA LYS PHE ILE LYS LYS ARG ARG THR LYS SER SEQRES 5 A 278 SER ARG ARG GLY VAL SER ARG GLU ASP ILE GLU ARG GLU SEQRES 6 A 278 VAL SER ILE LEU LYS GLU ILE GLN HIS PRO ASN VAL ILE SEQRES 7 A 278 THR LEU HIS GLU VAL TYR GLU ASN LYS THR ASP VAL ILE SEQRES 8 A 278 LEU ILE LEU GLU LEU VAL ALA GLY GLY GLU LEU PHE ASP SEQRES 9 A 278 PHE LEU ALA GLU LYS GLU SER LEU THR GLU GLU GLU ALA SEQRES 10 A 278 THR GLU PHE LEU LYS GLN ILE LEU ASN GLY VAL TYR TYR SEQRES 11 A 278 LEU HIS SER LEU GLN ILE ALA HIS PHE ASP LEU LYS PRO SEQRES 12 A 278 GLU ASN ILE MET LEU LEU ASP ARG ASN VAL PRO LYS PRO SEQRES 13 A 278 ARG ILE LYS ILE ILE ASP PHE GLY LEU ALA HIS LYS ILE SEQRES 14 A 278 ASP PHE GLY ASN GLU PHE LYS ASN ILE PHE GLY THR PRO SEQRES 15 A 278 GLU PHE VAL ALA PRO GLU ILE VAL ASN TYR GLU PRO LEU SEQRES 16 A 278 GLY LEU GLU ALA ASP MET TRP SER ILE GLY VAL ILE THR SEQRES 17 A 278 TYR ILE LEU LEU SER GLY ALA SER PRO PHE LEU GLY ASP SEQRES 18 A 278 THR LYS GLN GLU THR LEU ALA ASN VAL SER ALA VAL ASN SEQRES 19 A 278 TYR GLU PHE GLU ASP GLU TYR PHE SER ASN THR SER ALA SEQRES 20 A 278 LEU ALA LYS ASP PHE ILE ARG ARG LEU LEU VAL LYS ASP SEQRES 21 A 278 PRO LYS LYS ARG MET THR ILE GLN ASP SER LEU GLN HIS SEQRES 22 A 278 PRO TRP ILE LYS PRO HET SO4 A 301 5 HET SO4 A 302 5 HET SO4 A 303 5 HET SO4 A 304 5 HET NA A 305 1 HET GOL A 306 14 HET GOL A 307 14 HET GOL A 308 14 HET GOL A 309 14 HET GOL A 310 14 HET GOL A 311 14 HET NA A 312 1 HET MG A 313 1 HETNAM SO4 SULFATE ION HETNAM NA SODIUM ION HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 SO4 4(O4 S 2-) FORMUL 6 NA 2(NA 1+) FORMUL 7 GOL 6(C3 H8 O3) FORMUL 14 MG MG 2+ FORMUL 15 HOH *489(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 LYS A 108 1 9 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 ALA A 231 1 11 HELIX 10 AB1 GLU A 237 SER A 242 1 6 HELIX 11 AB2 SER A 245 LEU A 256 1 12 HELIX 12 AB3 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 PHE A 43 N VAL A 26 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 HIS A 80 O ILE A 92 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 LINK OE1 GLU A 32 NA NA A 305 1555 1555 2.62 LINK OH TYR A 39 NA NA A 305 1555 1555 2.67 LINK OE1 GLN A 72 NA NA A 312 1555 1555 1.93 LINK OG SER A 132 NA NA A 305 1555 4455 2.90 LINK O ASP A 169 NA NA A 312 1555 4455 2.71 LINK NA NA A 312 O HOH A 402 1555 1555 3.19 LINK NA NA A 312 O HOH A 497 1555 1555 2.87 LINK MG MG A 313 O HOH A 870 1555 1555 2.29 SITE 1 AC1 7 LYS A 86 LYS A 249 ARG A 253 GOL A 309 SITE 2 AC1 7 HOH A 488 HOH A 553 HOH A 880 SITE 1 AC2 4 LYS A 222 LEU A 226 ARG A 254 HOH A 801 SITE 1 AC3 8 GLY A 22 GLN A 23 HOH A 712 HOH A 720 SITE 2 AC3 8 HOH A 791 HOH A 815 HOH A 833 HOH A 843 SITE 1 AC4 4 ARG A 63 HOH A 682 HOH A 717 HOH A 766 SITE 1 AC5 6 GLU A 32 THR A 35 LEU A 37 TYR A 39 SITE 2 AC5 6 HIS A 80 SER A 132 SITE 1 AC6 9 ALA A 40 GLU A 94 LEU A 95 VAL A 96 SITE 2 AC6 9 MET A 146 ILE A 160 HOH A 783 HOH A 831 SITE 3 AC6 9 HOH A 870 SITE 1 AC7 10 PHE A 102 PRO A 142 GLU A 143 GLU A 182 SITE 2 AC7 10 PHE A 183 ILE A 209 HOH A 750 HOH A 751 SITE 3 AC7 10 HOH A 772 HOH A 885 SITE 1 AC8 8 LYS A 42 VAL A 56 GLU A 64 ASP A 161 SITE 2 AC8 8 HOH A 681 HOH A 718 HOH A 720 HOH A 833 SITE 1 AC9 8 TYR A 234 GLU A 235 PHE A 236 ARG A 253 SITE 2 AC9 8 SO4 A 301 HOH A 407 HOH A 553 HOH A 834 SITE 1 AD1 7 VAL A 26 ASP A 88 ASN A 243 HOH A 467 SITE 2 AD1 7 HOH A 518 HOH A 547 HOH A 868 SITE 1 AD2 12 ARG A 5 TYR A 12 GLU A 32 SER A 34 SITE 2 AD2 12 TYR A 128 GLN A 271 HOH A 403 HOH A 404 SITE 3 AD2 12 HOH A 411 HOH A 451 HOH A 512 HOH A 672 SITE 1 AD3 4 GLN A 72 HIS A 73 ASP A 169 HOH A 497 SITE 1 AD4 3 LYS A 42 ASP A 161 HOH A 870 CRYST1 46.516 62.005 88.375 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 0.021498 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016128 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011315 0.00000