PDB Short entry for 1FAO HEADER SIGNALING PROTEIN 13-JUL-00 1FAO TITLE STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN FROM DAPP1/PHISH IN TITLE 2 COMPLEX WITH INOSITOL 1,3,4,5-TETRAKISPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUAL ADAPTOR OF PHOSPHOTYROSINE AND 3-PHOSPHOINOSITIDES; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PLECKSTRIN HOMOLOGY DOMAIN; COMPND 5 SYNONYM: DAPP1, PHISH, BAM32; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: COMPLEX WITH INOSITOL 1,3,4,5-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 SIGNAL KEYWDS 2 TRANSDUCTION PROTEIN, ADAPTOR PROTEIN, SIGNALING 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 5 09-AUG-23 1FAO 1 REMARK 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,S.J.ISAKOFF, JRNL AUTH 2 E.Y.SKOLNIK,M.A.LEMMON JRNL TITL STRUCTURAL BASIS FOR DISCRIMINATION OF 3-PHOSPHOINOSITIDES JRNL TITL 2 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 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) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.720 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. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUL-00. REMARK 100 THE DEPOSITION ID IS D_1000011440. 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> FOR SHELL : 29.00 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