HEADER SIGNALING PROTEIN 27-JUL-04 1U5D TITLE CRYSTAL STRUCTURE OF THE PH DOMAIN OF SKAP55 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SRC KINASE-ASSOCIATED PHOSPHOPROTEIN OF 55 KDA; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: PH DOMAIN (RESIDUES 106-213); COMPND 5 SYNONYM: SKAP55; 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: HSSKAP55; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS PH DOMAIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.TANG,K.D.SWANSON,B.G.NEEL,M.J.ECK REVDAT 4 23-AUG-23 1U5D 1 REMARK REVDAT 3 20-OCT-21 1U5D 1 REMARK SEQADV REVDAT 2 24-FEB-09 1U5D 1 VERSN REVDAT 1 26-JUL-05 1U5D 0 JRNL AUTH Y.TANG,K.D.SWANSON,B.G.NEEL,M.J.ECK JRNL TITL STRUCTURAL BASIS FOR THE DIMERIZATION AND PHOSPHOINOSITIDE JRNL TITL 2 SPECIFICITY OF THE SRC KINASE-ASSOCIATED PHOSPHOPROTEINS JRNL TITL 3 SKAP55 AND SKAP-HOM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.8 REMARK 3 NUMBER OF REFLECTIONS : 45007 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2334 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2060 REMARK 3 BIN FREE R VALUE SET COUNT : 65 REMARK 3 BIN FREE R VALUE : 0.2590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3578 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 427 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.80 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; 0.019 ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; 1.800 ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1U5D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUL-04. REMARK 100 THE DEPOSITION ID IS D_1000023265. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 8-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45007 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.2 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 40.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.18300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 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: STRUCTURE OF THE PH DOMAIN OF SKAP-HOM, PDB ENTRY REMARK 200 1U5G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, SODIUM ACETATE, PH REMARK 280 5.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 16.67600 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5, 6, 7, 8, 9 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 REMARK 350 BIOMOLECULE: 5 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -132.0 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 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 -74.06800 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 350 APPLY THE FOLLOWING TO CHAINS: C REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 -37.48998 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 -33.35200 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -98.83023 REMARK 350 APPLY THE FOLLOWING TO CHAINS: D REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 -37.48998 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 -98.83023 REMARK 350 REMARK 350 BIOMOLECULE: 6 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -127.0 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 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 -74.06800 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 350 APPLY THE FOLLOWING TO CHAINS: C REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 37.48998 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 -50.02800 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 98.83023 REMARK 350 APPLY THE FOLLOWING TO CHAINS: D REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 37.48998 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 -16.67600 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 98.83023 REMARK 350 REMARK 350 BIOMOLECULE: 7 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -59.0 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 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 -74.06800 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 350 REMARK 350 BIOMOLECULE: 8 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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: D REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 33.35200 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 9 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -53.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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: B REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 -36.57802 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 33.35200 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 98.83023 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 SER B 213 REMARK 465 SER C 213 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 ARG A 169 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ASP A 184 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP B 184 CB - CG - OD2 ANGL. DEV. = 9.5 DEGREES REMARK 500 ASP D 120 CB - CG - OD2 ANGL. DEV. = 7.1 DEGREES REMARK 500 ARG D 163 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG D 199 NE - CZ - NH1 ANGL. DEV. = 7.5 DEGREES REMARK 500 ARG D 199 NE - CZ - NH2 ANGL. DEV. = -8.8 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 SER A 122 -145.30 -153.40 REMARK 500 LYS B 210 -63.57 -21.11 REMARK 500 SER C 122 80.02 68.47 REMARK 500 PHE C 123 64.12 -58.99 REMARK 500 LYS D 119 168.50 -48.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PHE C 123 PHE C 124 148.61 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 SO4 C 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1007 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1U5G RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PH DOMAIN OF SKAP-HOM REMARK 900 RELATED ID: 1U5E RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A N-TERMINAL FRAGMENT OF SKAP-HOM CONTAINING REMARK 900 BOTH THE HELICAL DIMERIZATION DOMAIN AND THE PH DOMAIN REMARK 900 RELATED ID: 1U5F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PH DOMAIN OF SKAP-HOM WITH 8 VECTOR- REMARK 900 DERIVED N-TERMINAL RESIDUES. DBREF 1U5D A 106 213 UNP O15268 O15268_HUMAN 106 213 DBREF 1U5D B 106 213 UNP O15268 O15268_HUMAN 106 213 DBREF 1U5D C 106 213 UNP O15268 O15268_HUMAN 106 213 DBREF 1U5D D 106 213 UNP O15268 O15268_HUMAN 106 213 SEQADV 1U5D GLY A 106 UNP O15268 ASP 106 ENGINEERED MUTATION SEQADV 1U5D SER A 107 UNP O15268 ASN 107 ENGINEERED MUTATION SEQADV 1U5D GLY B 106 UNP O15268 ASP 106 ENGINEERED MUTATION SEQADV 1U5D SER B 107 UNP O15268 ASN 107 ENGINEERED MUTATION SEQADV 1U5D GLY C 106 UNP O15268 ASP 106 ENGINEERED MUTATION SEQADV 1U5D SER C 107 UNP O15268 ASN 107 ENGINEERED MUTATION SEQADV 1U5D GLY D 106 UNP O15268 ASP 106 ENGINEERED MUTATION SEQADV 1U5D SER D 107 UNP O15268 ASN 107 ENGINEERED MUTATION SEQRES 1 A 108 GLY SER VAL ILE LYS GLN GLY TYR LEU GLU LYS LYS SER SEQRES 2 A 108 LYS ASP HIS SER PHE PHE GLY SER GLU TRP GLN LYS ARG SEQRES 3 A 108 TRP CYS VAL VAL SER ARG GLY LEU PHE TYR TYR TYR ALA SEQRES 4 A 108 ASN GLU LYS SER LYS GLN PRO LYS GLY THR PHE LEU ILE SEQRES 5 A 108 LYS GLY TYR SER VAL ARG MET ALA PRO HIS LEU ARG ARG SEQRES 6 A 108 ASP SER LYS LYS GLU SER CYS PHE GLU LEU THR SER GLN SEQRES 7 A 108 ASP ARG ARG THR TYR GLU PHE THR ALA THR SER PRO ALA SEQRES 8 A 108 GLU ALA ARG ASP TRP VAL ASP GLN ILE SER PHE LEU LEU SEQRES 9 A 108 LYS ASP LEU SER SEQRES 1 B 108 GLY SER VAL ILE LYS GLN GLY TYR LEU GLU LYS LYS SER SEQRES 2 B 108 LYS ASP HIS SER PHE PHE GLY SER GLU TRP GLN LYS ARG SEQRES 3 B 108 TRP CYS VAL VAL SER ARG GLY LEU PHE TYR TYR TYR ALA SEQRES 4 B 108 ASN GLU LYS SER LYS GLN PRO LYS GLY THR PHE LEU ILE SEQRES 5 B 108 LYS GLY TYR SER VAL ARG MET ALA PRO HIS LEU ARG ARG SEQRES 6 B 108 ASP SER LYS LYS GLU SER CYS PHE GLU LEU THR SER GLN SEQRES 7 B 108 ASP ARG ARG THR TYR GLU PHE THR ALA THR SER PRO ALA SEQRES 8 B 108 GLU ALA ARG ASP TRP VAL ASP GLN ILE SER PHE LEU LEU SEQRES 9 B 108 LYS ASP LEU SER SEQRES 1 C 108 GLY SER VAL ILE LYS GLN GLY TYR LEU GLU LYS LYS SER SEQRES 2 C 108 LYS ASP HIS SER PHE PHE GLY SER GLU TRP GLN LYS ARG SEQRES 3 C 108 TRP CYS VAL VAL SER ARG GLY LEU PHE TYR TYR TYR ALA SEQRES 4 C 108 ASN GLU LYS SER LYS GLN PRO LYS GLY THR PHE LEU ILE SEQRES 5 C 108 LYS GLY TYR SER VAL ARG MET ALA PRO HIS LEU ARG ARG SEQRES 6 C 108 ASP SER LYS LYS GLU SER CYS PHE GLU LEU THR SER GLN SEQRES 7 C 108 ASP ARG ARG THR TYR GLU PHE THR ALA THR SER PRO ALA SEQRES 8 C 108 GLU ALA ARG ASP TRP VAL ASP GLN ILE SER PHE LEU LEU SEQRES 9 C 108 LYS ASP LEU SER SEQRES 1 D 108 GLY SER VAL ILE LYS GLN GLY TYR LEU GLU LYS LYS SER SEQRES 2 D 108 LYS ASP HIS SER PHE PHE GLY SER GLU TRP GLN LYS ARG SEQRES 3 D 108 TRP CYS VAL VAL SER ARG GLY LEU PHE TYR TYR TYR ALA SEQRES 4 D 108 ASN GLU LYS SER LYS GLN PRO LYS GLY THR PHE LEU ILE SEQRES 5 D 108 LYS GLY TYR SER VAL ARG MET ALA PRO HIS LEU ARG ARG SEQRES 6 D 108 ASP SER LYS LYS GLU SER CYS PHE GLU LEU THR SER GLN SEQRES 7 D 108 ASP ARG ARG THR TYR GLU PHE THR ALA THR SER PRO ALA SEQRES 8 D 108 GLU ALA ARG ASP TRP VAL ASP GLN ILE SER PHE LEU LEU SEQRES 9 D 108 LYS ASP LEU SER HET SO4 A1002 5 HET SO4 A1007 5 HET SO4 B1004 5 HET SO4 C1001 5 HET SO4 C1003 5 HET SO4 D1005 5 HET SO4 D1006 5 HETNAM SO4 SULFATE ION FORMUL 5 SO4 7(O4 S 2-) FORMUL 12 HOH *427(H2 O) HELIX 1 1 PRO A 166 ARG A 169 5 4 HELIX 2 2 ASP A 171 GLU A 175 5 5 HELIX 3 3 SER A 194 SER A 213 1 20 HELIX 4 4 ASP B 171 GLU B 175 5 5 HELIX 5 5 SER B 194 LYS B 210 1 17 HELIX 6 6 ASP C 171 GLU C 175 5 5 HELIX 7 7 SER C 194 LYS C 210 1 17 HELIX 8 8 PRO D 166 ARG D 169 5 4 HELIX 9 9 ASP D 171 GLU D 175 5 5 HELIX 10 10 SER D 194 SER D 213 1 20 SHEET 1 A 7 GLY A 153 LEU A 156 0 SHEET 2 A 7 LEU A 139 TYR A 143 -1 N PHE A 140 O PHE A 155 SHEET 3 A 7 SER A 126 SER A 136 -1 N VAL A 134 O TYR A 141 SHEET 4 A 7 VAL A 108 LYS A 119 -1 N LYS A 110 O VAL A 135 SHEET 5 A 7 TYR A 188 THR A 191 -1 O THR A 191 N GLU A 115 SHEET 6 A 7 CYS A 177 THR A 181 -1 N LEU A 180 O TYR A 188 SHEET 7 A 7 SER A 161 MET A 164 -1 N ARG A 163 O GLU A 179 SHEET 1 B 7 GLY B 153 LEU B 156 0 SHEET 2 B 7 LEU B 139 TYR B 143 -1 N PHE B 140 O PHE B 155 SHEET 3 B 7 TRP B 128 SER B 136 -1 N VAL B 134 O TYR B 141 SHEET 4 B 7 VAL B 108 LYS B 117 -1 N LEU B 114 O ARG B 131 SHEET 5 B 7 TYR B 188 THR B 191 -1 O THR B 191 N GLU B 115 SHEET 6 B 7 CYS B 177 SER B 182 -1 N PHE B 178 O PHE B 190 SHEET 7 B 7 TYR B 160 MET B 164 -1 N ARG B 163 O GLU B 179 SHEET 1 C 7 GLY C 153 LEU C 156 0 SHEET 2 C 7 LEU C 139 TYR C 143 -1 N PHE C 140 O PHE C 155 SHEET 3 C 7 TRP C 128 SER C 136 -1 N VAL C 134 O TYR C 141 SHEET 4 C 7 VAL C 108 LYS C 117 -1 N LEU C 114 O ARG C 131 SHEET 5 C 7 TYR C 188 THR C 191 -1 O THR C 191 N GLU C 115 SHEET 6 C 7 CYS C 177 SER C 182 -1 N LEU C 180 O TYR C 188 SHEET 7 C 7 TYR C 160 MET C 164 -1 N ARG C 163 O GLU C 179 SHEET 1 D 7 GLY D 153 LEU D 156 0 SHEET 2 D 7 LEU D 139 TYR D 143 -1 N PHE D 140 O PHE D 155 SHEET 3 D 7 TRP D 128 SER D 136 -1 N SER D 136 O LEU D 139 SHEET 4 D 7 VAL D 108 LYS D 117 -1 N GLY D 112 O CYS D 133 SHEET 5 D 7 ARG D 185 THR D 191 -1 O THR D 191 N GLU D 115 SHEET 6 D 7 CYS D 177 SER D 182 -1 N PHE D 178 O PHE D 190 SHEET 7 D 7 SER D 161 MET D 164 -1 N ARG D 163 O GLU D 179 SITE 1 AC1 8 ARG B 163 ALA B 165 PRO B 166 HIS B 167 SITE 2 AC1 8 ARG C 163 ALA C 165 PRO C 166 HIS C 167 SITE 1 AC2 8 LYS A 116 SER A 118 ARG A 131 TYR A 142 SITE 2 AC2 8 LYS A 152 SO4 A1007 HOH A1051 HOH A1094 SITE 1 AC3 6 LYS C 116 LYS C 119 ARG C 131 TYR C 142 SITE 2 AC3 6 LYS C 152 HOH C1101 SITE 1 AC4 5 LYS B 116 ARG B 131 TYR B 142 LYS B 152 SITE 2 AC4 5 HOH B1018 SITE 1 AC5 3 THR D 187 HOH D1042 HOH D1086 SITE 1 AC6 7 LYS D 116 LYS D 119 GLN D 129 ARG D 131 SITE 2 AC6 7 TYR D 142 LYS D 152 HOH D1084 SITE 1 AC7 10 LYS A 116 LYS A 117 SER A 118 LYS A 119 SITE 2 AC7 10 HIS A 121 ARG A 186 SO4 A1002 HOH A1051 SITE 3 AC7 10 HOH A1059 HOH A1105 CRYST1 74.068 33.352 105.382 90.00 110.31 90.00 P 1 21 1 8 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 0.013501 0.000000 0.004997 0.00000 SCALE2 0.000000 0.029983 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010118 0.00000