PDB Short entry for 1PHT HEADER PHOSPHOTRANSFERASE 17-AUG-95 1PHT TITLE PHOSPHATIDYLINOSITOL 3-KINASE P85-ALPHA SUBUNIT SH3 DOMAIN, RESIDUES TITLE 2 1-85 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHATIDYLINOSITOL 3-KINASE P85-ALPHA SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PI3K SH3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL_LINE: BL21(DE3); SOURCE 6 GENE: PI3K SH3 FROM CDNA LIBRARY OF; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PLM1-SH3; SOURCE 11 EXPRESSION_SYSTEM_GENE: PI3K SH3 FROM CDNA LIBRARY OF; SOURCE 12 OTHER_DETAILS: NOVAGEN KEYWDS PHOSPHATIDYLINOSITOL 3-KINASE, P85-ALPHA SUBUNIT, SH3 DOMAIN, KEYWDS 2 PHOSPHOTRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.LIANG,J.K.CHEN,S.L.SCHREIBER,J.CLARDY REVDAT 3 14-FEB-24 1PHT 1 REMARK REVDAT 2 24-FEB-09 1PHT 1 VERSN REVDAT 1 07-DEC-95 1PHT 0 JRNL AUTH J.LIANG,J.K.CHEN,S.T.SCHREIBER,J.CLARDY JRNL TITL CRYSTAL STRUCTURE OF P13K SH3 DOMAIN AT 20 ANGSTROMS JRNL TITL 2 RESOLUTION. JRNL REF J.MOL.BIOL. V. 257 632 1996 JRNL REFN ISSN 0022-2836 JRNL PMID 8648629 JRNL DOI 10.1006/JMBI.1996.0190 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.YU,J.K.CHEN,D.C.DALGARNO,A.W.BRAUER,S.L.SCHREIBER REMARK 1 TITL STRUCTURAL BASIS FOR THE BINDING OF PROLINE-RICH PEPTIDES TO REMARK 1 TITL 2 SH3 DOMAINS REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 76 933 1994 REMARK 1 REFN ISSN 0092-8674 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 6918 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 666 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 59 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.10 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.00 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.367 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.02 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.205 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 SOLVENT MOLECULES WITH TEMPERATURE FACTORS GREATER THAN 50 REMARK 3 ANGSTROMS**2 MAY NOT BE WELL DEFINED. REMARK 4 REMARK 4 1PHT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000175686. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-APR-95 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : XUONG-HAMLIN MULTIWIRE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6918 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 8.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.03500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.15000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 23.50000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 23.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 69.22500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 23.50000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 23.50000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 23.07500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 23.50000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 23.50000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 69.22500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 23.50000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 23.50000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 23.07500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 46.15000 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: SYMMETRY REMARK 300 THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED REMARK 300 BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. REMARK 300 REMARK 300 APPLIED TO RESIDUES: 3 .. 85 REMARK 300 SYMMETRY1 1 -1.000000 0.000000 0.000000 3.00000 REMARK 300 SYMMETRY2 1 0.000000 1.000000 0.000000 1.00000 REMARK 300 SYMMETRY3 1 0.000000 0.000000 -1.000000 3.00000 REMARK 300 REMARK 300 SYMMETRY1 2 0.000000 1.000000 0.000000 0.00000 REMARK 300 SYMMETRY2 2 1.000000 0.000000 0.000000 0.00000 REMARK 300 SYMMETRY3 2 0.000000 0.000000 -1.000000 1.00000 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 SER A 2 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 44 -126.25 59.09 REMARK 500 REMARK 500 REMARK: NULL DBREF 1PHT A 1 85 UNP P27986 P85A_HUMAN 1 85 SEQRES 1 A 85 MET SER ALA GLU GLY TYR GLN TYR ARG ALA LEU TYR ASP SEQRES 2 A 85 TYR LYS LYS GLU ARG GLU GLU ASP ILE ASP LEU HIS LEU SEQRES 3 A 85 GLY ASP ILE LEU THR VAL ASN LYS GLY SER LEU VAL ALA SEQRES 4 A 85 LEU GLY PHE SER ASP GLY GLN GLU ALA ARG PRO GLU GLU SEQRES 5 A 85 ILE GLY TRP LEU ASN GLY TYR ASN GLU THR THR GLY GLU SEQRES 6 A 85 ARG GLY ASP PHE PRO GLY THR TYR VAL GLU TYR ILE GLY SEQRES 7 A 85 ARG LYS LYS ILE SER PRO PRO FORMUL 2 HOH *59(H2 O) HELIX 1 1 LYS A 34 LEU A 40 1 7 HELIX 2 2 GLN A 46 ALA A 48 5 3 HELIX 3 3 PRO A 50 ILE A 53 1 4 HELIX 4 4 GLY A 71 TYR A 73 5 3 SHEET 1 A 3 ILE A 29 ASN A 33 0 SHEET 2 A 3 GLU A 4 ALA A 10 -1 N TYR A 8 O LEU A 30 SHEET 3 A 3 VAL A 74 LYS A 81 -1 N LYS A 80 O GLY A 5 SHEET 1 B 2 TRP A 55 ASN A 60 0 SHEET 2 B 2 GLU A 65 PRO A 70 -1 N PHE A 69 O LEU A 56 CRYST1 47.000 47.000 92.300 90.00 90.00 90.00 P 43 21 2 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 0.021277 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021277 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010834 0.00000