HEADER SIGNALING PROTEIN 13-JUL-00 1FAO TITLE STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN FROM TITLE 2 DAPP1/PHISH IN COMPLEX WITH INOSITOL 1,3,4,5- TITLE 3 TETRAKISPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUAL ADAPTOR OF PHOSPHOTYROSINE AND 3- COMPND 3 PHOSPHOINOSITIDES; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: PLECKSTRIN HOMOLOGY DOMAIN; COMPND 6 SYNONYM: DAPP1, PHISH, BAM32; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: COMPLEX WITH INOSITOL 1,3,4,5- COMPND 9 TETRAKISPHOSPHATE 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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS PLECKSTRIN, 3-PHOSPHOINOSITIDES, INOSITOL TETRAKISPHOSPHATE KEYWDS 2 SIGNAL TRANSDUCTION PROTEIN, ADAPTOR PROTEIN, SIGNALING KEYWDS 3 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.M.FERGUSON,J.M.KAVRAN,V.G.SANKARAN,E.FOURNIER,S.J.ISAKOFF, AUTHOR 2 E.Y.SKOLNIK,M.A.LEMMON REVDAT 4 24-FEB-09 1FAO 1 VERSN REVDAT 3 29-NOV-00 1FAO 1 JRNL REVDAT 2 16-AUG-00 1FAO 1 COMPND REVDAT 1 20-JUL-00 1FAO 0 JRNL AUTH K.M.FERGUSON,J.M.KAVRAN,V.G.SANKARAN,E.FOURNIER, JRNL AUTH 2 S.J.ISAKOFF,E.Y.SKOLNIK,M.A.LEMMON JRNL TITL STRUCTURAL BASIS FOR DISCRIMINATION OF JRNL TITL 2 3-PHOSPHOINOSITIDES BY PLECKSTRIN HOMOLOGY DOMAINS. JRNL REF MOL.CELL V. 6 373 2000 JRNL REFN ISSN 1097-2765 JRNL PMID 10983984 JRNL DOI 10.1016/S1097-2765(00)00037-X REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 11421 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) : 0.219 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.500 REMARK 3 FREE R VALUE TEST SET COUNT : 1083 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1722 REMARK 3 BIN R VALUE (WORKING SET) : 0.2260 REMARK 3 BIN FREE R VALUE : 0.2770 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 201 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 838 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 105 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.51000 REMARK 3 B22 (A**2) : -2.97000 REMARK 3 B33 (A**2) : 0.46000 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) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.03 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) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.13 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.72 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) : 1.620 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.010 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.720 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.450 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 40.12 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_REP.PARAM REMARK 3 PARAMETER FILE 3 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 4 : PARAM.IP4 REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 4 : TOP.IP4 REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1FAO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUL-00. REMARK 100 THE RCSB ID CODE IS RCSB011440. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRANDEIS - B4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11260 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : 0.04000 REMARK 200 FOR THE DATA SET : 26.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.05000 REMARK 200 R SYM FOR SHELL (I) : 0.05000 REMARK 200 FOR SHELL : 29.000 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: PDB ID 1FB8: UNLIGANDED DAPP1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3450, TRIS, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 20.33700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.37150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.13650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.37150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.33700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.13650 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: THE BIOLOGICAL ASSEMBLY IS A MONOMER 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 148 REMARK 465 GLN A 149 REMARK 465 THR A 150 REMARK 465 GLY A 151 REMARK 465 ARG A 152 REMARK 465 THR A 153 REMARK 465 GLU A 154 REMARK 465 ASP A 155 REMARK 465 ASP A 156 REMARK 465 LEU A 157 REMARK 465 VAL A 158 REMARK 465 PRO A 159 REMARK 465 THR A 160 REMARK 465 ALA A 161 REMARK 465 ARG A 262 REMARK 465 LYS A 263 REMARK 465 GLN A 264 REMARK 465 LEU A 265 REMARK 465 ASN A 266 REMARK 465 GLN A 267 REMARK 465 GLY A 268 REMARK 465 GLU A 269 REMARK 465 GLY A 270 REMARK 465 THR A 271 REMARK 465 ILE A 272 REMARK 465 ARG A 273 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 LYS A 179 44.91 -80.83 REMARK 500 ARG A 190 -126.76 55.69 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 4IP A 274 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FB8 RELATED DB: PDB REMARK 900 STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN FROM DAPP1/PHISH DBREF 1FAO A 148 273 UNP Q9UN19 DAPP1_HUMAN 148 273 SEQRES 1 A 126 MET GLN THR GLY ARG THR GLU ASP ASP LEU VAL PRO THR SEQRES 2 A 126 ALA PRO SER LEU GLY THR LYS GLU GLY TYR LEU THR LYS SEQRES 3 A 126 GLN GLY GLY LEU VAL LYS THR TRP LYS THR ARG TRP PHE SEQRES 4 A 126 THR LEU HIS ARG ASN GLU LEU LYS TYR PHE LYS ASP GLN SEQRES 5 A 126 MET SER PRO GLU PRO ILE ARG ILE LEU ASP LEU THR GLU SEQRES 6 A 126 CYS SER ALA VAL GLN PHE ASP TYR SER GLN GLU ARG VAL SEQRES 7 A 126 ASN CYS PHE CYS LEU VAL PHE PRO PHE ARG THR PHE TYR SEQRES 8 A 126 LEU CYS ALA LYS THR GLY VAL GLU ALA ASP GLU TRP ILE SEQRES 9 A 126 LYS ILE LEU ARG TRP LYS LEU SER GLN ILE ARG LYS GLN SEQRES 10 A 126 LEU ASN GLN GLY GLU GLY THR ILE ARG HET 4IP A 274 28 HETNAM 4IP INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE FORMUL 2 4IP C6 H16 O18 P4 FORMUL 3 HOH *105(H2 O) HELIX 1 1 THR A 211 CYS A 213 5 3 HELIX 2 2 THR A 243 GLN A 260 1 18 SHEET 1 A 7 ARG A 206 ASP A 209 0 SHEET 2 A 7 GLU A 192 PHE A 196 -1 N LEU A 193 O LEU A 208 SHEET 3 A 7 TRP A 181 HIS A 189 -1 O TRP A 185 N PHE A 196 SHEET 4 A 7 LYS A 167 GLN A 174 -1 O LYS A 167 N LEU A 188 SHEET 5 A 7 ARG A 235 CYS A 240 -1 O TYR A 238 N GLN A 174 SHEET 6 A 7 CYS A 227 PHE A 232 -1 O PHE A 228 N LEU A 239 SHEET 7 A 7 ALA A 215 ASP A 219 -1 O ALA A 215 N VAL A 231 SSBOND 1 CYS A 227 CYS A 240 1555 1555 2.04 SITE 1 AC1 21 HOH A 1 HOH A 31 HOH A 57 HOH A 64 SITE 2 AC1 21 HOH A 80 HOH A 91 HOH A 102 HOH A 103 SITE 3 AC1 21 LYS A 173 GLY A 175 GLY A 176 LEU A 177 SITE 4 AC1 21 VAL A 178 THR A 180 LYS A 182 ARG A 184 SITE 5 AC1 21 TYR A 195 LYS A 197 ILE A 205 ARG A 235 SITE 6 AC1 21 LYS A 242 CRYST1 40.674 46.273 64.743 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 0.024586 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021611 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015446 0.00000 MASTER 279 0 1 2 7 0 6 6 0 0 0 10 END