HEADER TRANSFERASE 24-MAY-00 1F2F TITLE SRC SH2 THREF1TRP MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SH2 DOMAIN; COMPND 5 EC: 2.7.1.112; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-11D KEYWDS SRC, SH2 DOMAIN, SPECIFICITY SWITCH, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.S.KIMBER,J.NACHMAN,A.M.CUNNINGHAM,G.D.GISH,T.PAWSON,E.F.PAI REVDAT 4 07-FEB-24 1F2F 1 REMARK REVDAT 3 03-NOV-21 1F2F 1 REMARK SEQADV REVDAT 2 24-FEB-09 1F2F 1 VERSN REVDAT 1 06-JUL-00 1F2F 0 JRNL AUTH M.S.KIMBER,J.NACHMAN,A.M.CUNNINGHAM,G.D.GISH,T.PAWSON, JRNL AUTH 2 E.F.PAI JRNL TITL STRUCTURAL BASIS FOR SPECIFICITY SWITCHING OF THE SRC SH2 JRNL TITL 2 DOMAIN. JRNL REF MOL.CELL V. 5 1043 2000 JRNL REFN ISSN 1097-2765 JRNL PMID 10911998 JRNL DOI 10.1016/S1097-2765(00)80269-5 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.3 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 281505.730 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 11658 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) : 0.208 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.400 REMARK 3 FREE R VALUE TEST SET COUNT : 1207 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1721 REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE : 0.2730 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 219 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 849 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 55 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.13000 REMARK 3 B22 (A**2) : -2.25000 REMARK 3 B33 (A**2) : 2.12000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.45000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.07 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) : 0.14 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.430 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) : 1.340 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.200 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.040 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.130 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 : PROTEIN.PARAM REMARK 3 PARAMETER FILE 2 : PO4.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : PO4.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1F2F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUN-00. REMARK 100 THE DEPOSITION ID IS D_1000011161. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUN-96 REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.885 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : STORAGE PHOSPHORS REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11664 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.5000 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) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.28300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM ACETATE,SODIUM REMARK 280 CACODYLATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 295.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 37.23000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 13.61000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 37.23000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 13.61000 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 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 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 152 44.31 -86.21 REMARK 500 ASP A 235 57.09 34.30 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 PO4 A 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1F1W RELATED DB: PDB REMARK 900 1F1W CONTAINS THE SAME PROTEIN COMPLEXED WITH THE PHOSPHOPEPTIDE REMARK 900 (PTR)VNV DBREF 1F2F A 145 247 UNP P00523 SRC_CHICK 144 246 SEQADV 1F2F MET A 144 UNP P00523 INITIATING METHIONINE SEQADV 1F2F TRP A 215 UNP P00523 THR 214 ENGINEERED MUTATION SEQRES 1 A 104 MET ALA GLU GLU TRP TYR PHE GLY LYS ILE THR ARG ARG SEQRES 2 A 104 GLU SER GLU ARG LEU LEU LEU ASN PRO GLU ASN PRO ARG SEQRES 3 A 104 GLY THR PHE LEU VAL ARG GLU SER GLU THR THR LYS GLY SEQRES 4 A 104 ALA TYR CYS LEU SER VAL SER ASP PHE ASP ASN ALA LYS SEQRES 5 A 104 GLY LEU ASN VAL LYS HIS TYR LYS ILE ARG LYS LEU ASP SEQRES 6 A 104 SER GLY GLY PHE TYR ILE TRP SER ARG THR GLN PHE SER SEQRES 7 A 104 SER LEU GLN GLN LEU VAL ALA TYR TYR SER LYS HIS ALA SEQRES 8 A 104 ASP GLY LEU CYS HIS ARG LEU THR ASN VAL CYS PRO THR HET PO4 A 300 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 O4 P 3- FORMUL 3 HOH *55(H2 O) HELIX 1 1 THR A 154 LEU A 163 1 10 HELIX 2 2 SER A 222 HIS A 233 1 12 SHEET 1 A 5 TRP A 148 PHE A 150 0 SHEET 2 A 5 THR A 171 SER A 177 1 SHEET 3 A 5 ALA A 183 ASP A 190 -1 SHEET 4 A 5 ASN A 198 ILE A 204 -1 SHEET 5 A 5 ASN A 243 CYS A 245 1 SHEET 1 B 3 ILE A 204 LEU A 207 0 SHEET 2 B 3 GLY A 211 ILE A 214 -1 SHEET 3 B 3 THR A 218 PHE A 220 -1 SITE 1 AC1 8 ARG A 155 ARG A 175 SER A 177 GLU A 178 SITE 2 AC1 8 THR A 179 CYS A 185 LYS A 203 HOH A 525 CRYST1 74.460 27.220 55.250 90.00 106.68 90.00 C 1 2 1 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 0.013430 0.000000 0.004024 0.00000 SCALE2 0.000000 0.036738 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018895 0.00000