HEADER SIGNAL TRANSDUCTION 07-JUL-97 1AOJ TITLE THE SH3 DOMAIN OF EPS8 EXISTS AS A NOVEL INTERTWINED DIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: EPS8; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SH3 DOMAIN; COMPND 5 SYNONYM: SRC HOMOLOGY DOMAIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SIGNAL TRANSDUCTION, SH3 DOMAIN, EPS8, PROLINE RICH PEPTIDE EXPDTA X-RAY DIFFRACTION AUTHOR K.V.R.KISHAN,M.E.NEWCOMER REVDAT 3 02-AUG-23 1AOJ 1 REMARK REVDAT 2 24-FEB-09 1AOJ 1 VERSN REVDAT 1 08-JUL-98 1AOJ 0 JRNL AUTH K.V.KISHAN,G.SCITA,W.T.WONG,P.P.DI FIORE,M.E.NEWCOMER JRNL TITL THE SH3 DOMAIN OF EPS8 EXISTS AS A NOVEL INTERTWINED DIMER. JRNL REF NAT.STRUCT.BIOL. V. 4 739 1997 JRNL REFN ISSN 1072-8368 JRNL PMID 9303002 JRNL DOI 10.1038/NSB0997-739 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH F.FAZIOLI,L.MINICHIELLO,V.MATOSKA,P.CASTAGNINO,T.MIKI, REMARK 1 AUTH 2 W.T.WONG,P.P.DI FIORE REMARK 1 TITL EPS8, A SUBSTRATE FOR THE EPIDERMAL GROWTH FACTOR RECEPTOR REMARK 1 TITL 2 KINASE, ENHANCES EGF-DEPENDENT MITOGENIC SIGNALS REMARK 1 REF EMBO J. V. 12 3799 1993 REMARK 1 REFN ISSN 0261-4189 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT 5E REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.4 REMARK 3 NUMBER OF REFLECTIONS : 2927 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : R-FREE THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 140 REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 984 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 35 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.005 ; 0.800 ; 1002 REMARK 3 BOND ANGLES (DEGREES) : 1.540 ; 1.300 ; 1343 REMARK 3 TORSION ANGLES (DEGREES) : 22.352; 0.000 ; 605 REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : 0.004 ; 2.000 ; 29 REMARK 3 GENERAL PLANES (A) : 0.007 ; 5.000 ; 140 REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : 0.017 ; 10.000; 37 REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : 0.68 REMARK 3 BSOL : 192.0 REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : TNT PROTGEO REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : TNT BCORREL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT FIRST STARTED WITH X-PLOR REMARK 3 SIMULATED ANNEALING PROTOCOL REMARK 4 REMARK 4 1AOJ 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_1000171064. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : FEB-96 REMARK 200 TEMPERATURE (KELVIN) : 300 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MSC/YALE MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3406 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 32.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : 0.39700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CCP4 (ALMN) REMARK 200 STARTING MODEL: PDB ENTRY 1SHF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 0.4M REMARK 280 SODIUM POTASSIUM TARTRATE, PH 7.5. PROTEIN CONC. 6MG/ML. REMARK 280 CRYSTALLIZATION TIME 2-3 WEEKS. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 65 CG CD OE1 OE2 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 ASP A 14 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 14 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP A 28 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP A 29 CB - CG - OD1 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP A 35 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP A 36 CB - CG - OD1 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP A 49 CB - CG - OD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP B 14 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP B 28 CB - CG - OD1 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP B 49 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 PRO B 64 C - N - CA ANGL. DEV. = 11.9 DEGREES REMARK 500 PRO B 64 C - N - CD ANGL. DEV. = -15.1 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 ASP A 36 58.07 32.42 REMARK 500 ARG A 37 15.46 54.63 REMARK 500 PRO A 64 51.31 -57.00 REMARK 500 ASN B 19 -142.28 -101.01 REMARK 500 ASP B 35 -178.73 68.05 REMARK 500 ARG B 38 -70.00 -68.27 REMARK 500 GLN B 39 75.41 47.95 REMARK 500 PRO B 64 -89.04 -21.68 REMARK 500 REMARK 500 REMARK: NULL DBREF 1AOJ A 6 65 UNP Q08509 EPS8_MOUSE 532 591 DBREF 1AOJ B 6 65 UNP Q08509 EPS8_MOUSE 532 591 SEQRES 1 A 60 LYS LYS TYR ALA LYS SER LYS TYR ASP PHE VAL ALA ARG SEQRES 2 A 60 ASN SER SER GLU LEU SER VAL MET LYS ASP ASP VAL LEU SEQRES 3 A 60 GLU ILE LEU ASP ASP ARG ARG GLN TRP TRP LYS VAL ARG SEQRES 4 A 60 ASN ALA SER GLY ASP SER GLY PHE VAL PRO ASN ASN ILE SEQRES 5 A 60 LEU ASP ILE MET ARG THR PRO GLU SEQRES 1 B 60 LYS LYS TYR ALA LYS SER LYS TYR ASP PHE VAL ALA ARG SEQRES 2 B 60 ASN SER SER GLU LEU SER VAL MET LYS ASP ASP VAL LEU SEQRES 3 B 60 GLU ILE LEU ASP ASP ARG ARG GLN TRP TRP LYS VAL ARG SEQRES 4 B 60 ASN ALA SER GLY ASP SER GLY PHE VAL PRO ASN ASN ILE SEQRES 5 B 60 LEU ASP ILE MET ARG THR PRO GLU FORMUL 3 HOH *35(H2 O) HELIX 1 1 ASN A 55 ILE A 57 5 3 HELIX 2 2 ASN B 55 ILE B 57 5 3 SHEET 1 A 2 LYS A 7 LYS A 10 0 SHEET 2 A 2 VAL A 30 ILE A 33 -1 N ILE A 33 O LYS A 7 SHEET 1 B 2 TRP A 40 ARG A 44 0 SHEET 2 B 2 SER A 50 PRO A 54 -1 N VAL A 53 O TRP A 41 SHEET 1 C 2 LYS B 7 LYS B 10 0 SHEET 2 C 2 VAL B 30 ILE B 33 -1 N ILE B 33 O LYS B 7 SHEET 1 D 2 TRP B 40 ARG B 44 0 SHEET 2 D 2 SER B 50 PRO B 54 -1 N VAL B 53 O TRP B 41 CRYST1 27.690 28.338 36.825 107.53 96.83 104.51 P 1 2 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 0.036114 0.009346 0.008035 0.00000 SCALE2 0.000000 0.036451 0.013370 0.00000 SCALE3 0.000000 0.000000 0.029131 0.00000