HEADER SIGNALING PROTEIN 22-JUN-05 2A28 TITLE ATOMIC-RESOLUTION CRYSTAL STRUCTURE OF THE SECOND SH3 DOMAIN OF YEAST TITLE 2 BZZ1 DETERMINED FROM A PSEUDOMEROHEDRALLY TWINNED CRYSTAL COMPND MOL_ID: 1; COMPND 2 MOLECULE: BZZ1 PROTEIN; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: SH3 DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PDEST-17 KEYWDS SH3 DOMAIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.KURSULA,I.KURSULA,F.LEHMANN,P.ZOU,Y.H.SONG,M.WILMANNS REVDAT 3 13-MAR-24 2A28 1 REMARK SEQADV REVDAT 2 24-FEB-09 2A28 1 VERSN REVDAT 1 12-SEP-06 2A28 0 JRNL AUTH P.KURSULA,I.KURSULA,F.LEHMANN,P.ZOU,Y.H.SONG,M.WILMANNS JRNL TITL STRUCTURAL GENOMICS OF YEAST SH3 DOMAINS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM, SELECTED TAKING INTO REMARK 3 ACCOUNT THE TWINNING OPERATOR REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.112 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.111 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.166 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 0.800 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 695 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 84806 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.107 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.106 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.163 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 0.800 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 629 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 76102 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1615 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 390 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2007.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1428.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 4 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 18238 REMARK 3 NUMBER OF RESTRAINTS : 21490 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 ANGLE DISTANCES (A) : 0.032 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.026 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.101 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.086 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.026 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.052 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.092 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE CRYSTAL FORM IS TWINNED BY THE REMARK 3 OPERATOR H,-K,-L, TWINNING FRACTION 37 %. REMARK 4 REMARK 4 2A28 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JUN-05. REMARK 100 THE DEPOSITION ID IS D_1000033400. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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) : 0.8126 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 84816 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.070 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.24100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PH 8.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 25.87000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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: 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 TYR A 7 CB - CG - CD2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG A 29 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ASP A 31 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 GLU B 4 OE1 - CD - OE2 ANGL. DEV. = -9.7 DEGREES REMARK 500 GLU C 10 OE1 - CD - OE2 ANGL. DEV. = -8.4 DEGREES REMARK 500 ARG C 29 CD - NE - CZ ANGL. DEV. = 10.6 DEGREES REMARK 500 ARG C 29 NE - CZ - NH1 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG C 29 NE - CZ - NH2 ANGL. DEV. = 4.6 DEGREES REMARK 500 ASP C 31 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP C 31 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ASP C 32 CB - CG - OD1 ANGL. DEV. = 9.0 DEGREES REMARK 500 TYR C 38 CB - CG - CD1 ANGL. DEV. = 4.0 DEGREES REMARK 500 TYR C 38 CG - CD1 - CE1 ANGL. DEV. = 5.7 DEGREES REMARK 500 TYR C 38 CG - CD2 - CE2 ANGL. DEV. = -5.2 DEGREES REMARK 500 TYR C 38 CD1 - CE1 - CZ ANGL. DEV. = -5.4 DEGREES REMARK 500 TYR C 38 CZ - CE2 - CD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 TYR C 52 CB - CG - CD1 ANGL. DEV. = 3.9 DEGREES REMARK 500 TYR D 9 CB - CG - CD2 ANGL. DEV. = 3.8 DEGREES REMARK 500 ASP D 15 CB - CG - OD1 ANGL. DEV. = -6.7 DEGREES REMARK 500 ARG D 29 CD - NE - CZ ANGL. DEV. = 11.0 DEGREES REMARK 500 ARG D 29 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 2A28 A 3 54 UNP P38822 BZZ1_YEAST 582 633 DBREF 2A28 B 3 54 UNP P38822 BZZ1_YEAST 582 633 DBREF 2A28 C 3 54 UNP P38822 BZZ1_YEAST 582 633 DBREF 2A28 D 3 54 UNP P38822 BZZ1_YEAST 582 633 SEQADV 2A28 GLY A 1 UNP P38822 CLONING ARTIFACT SEQADV 2A28 ALA A 2 UNP P38822 CLONING ARTIFACT SEQADV 2A28 GLY B 1 UNP P38822 CLONING ARTIFACT SEQADV 2A28 ALA B 2 UNP P38822 CLONING ARTIFACT SEQADV 2A28 GLY C 1 UNP P38822 CLONING ARTIFACT SEQADV 2A28 ALA C 2 UNP P38822 CLONING ARTIFACT SEQADV 2A28 GLY D 1 UNP P38822 CLONING ARTIFACT SEQADV 2A28 ALA D 2 UNP P38822 CLONING ARTIFACT SEQRES 1 A 54 GLY ALA MET GLU ALA ILE TYR ALA TYR GLU ALA GLN GLY SEQRES 2 A 54 ASP ASP GLU ILE SER ILE ASP PRO GLY ASP ILE ILE THR SEQRES 3 A 54 VAL ILE ARG GLY ASP ASP GLY SER GLY TRP THR TYR GLY SEQRES 4 A 54 GLU CYS ASP GLY LEU LYS GLY LEU PHE PRO THR SER TYR SEQRES 5 A 54 CYS LYS SEQRES 1 B 54 GLY ALA MET GLU ALA ILE TYR ALA TYR GLU ALA GLN GLY SEQRES 2 B 54 ASP ASP GLU ILE SER ILE ASP PRO GLY ASP ILE ILE THR SEQRES 3 B 54 VAL ILE ARG GLY ASP ASP GLY SER GLY TRP THR TYR GLY SEQRES 4 B 54 GLU CYS ASP GLY LEU LYS GLY LEU PHE PRO THR SER TYR SEQRES 5 B 54 CYS LYS SEQRES 1 C 54 GLY ALA MET GLU ALA ILE TYR ALA TYR GLU ALA GLN GLY SEQRES 2 C 54 ASP ASP GLU ILE SER ILE ASP PRO GLY ASP ILE ILE THR SEQRES 3 C 54 VAL ILE ARG GLY ASP ASP GLY SER GLY TRP THR TYR GLY SEQRES 4 C 54 GLU CYS ASP GLY LEU LYS GLY LEU PHE PRO THR SER TYR SEQRES 5 C 54 CYS LYS SEQRES 1 D 54 GLY ALA MET GLU ALA ILE TYR ALA TYR GLU ALA GLN GLY SEQRES 2 D 54 ASP ASP GLU ILE SER ILE ASP PRO GLY ASP ILE ILE THR SEQRES 3 D 54 VAL ILE ARG GLY ASP ASP GLY SER GLY TRP THR TYR GLY SEQRES 4 D 54 GLU CYS ASP GLY LEU LYS GLY LEU PHE PRO THR SER TYR SEQRES 5 D 54 CYS LYS FORMUL 5 HOH *390(H2 O) HELIX 1 1 SER B 51 CYS B 53 5 3 SHEET 1 A 5 LEU A 44 PRO A 49 0 SHEET 2 A 5 TRP A 36 CYS A 41 -1 N CYS A 41 O LEU A 44 SHEET 3 A 5 ILE A 24 ARG A 29 -1 N THR A 26 O GLU A 40 SHEET 4 A 5 ALA A 2 ALA A 5 -1 N MET A 3 O ILE A 25 SHEET 5 A 5 CYS A 53 LYS A 54 -1 O LYS A 54 N GLU A 4 SHEET 1 B 4 MET B 3 GLU B 4 0 SHEET 2 B 4 ILE B 24 ARG B 29 -1 O ILE B 25 N MET B 3 SHEET 3 B 4 TRP B 36 CYS B 41 -1 O GLU B 40 N THR B 26 SHEET 4 B 4 LEU B 44 PRO B 49 -1 O LEU B 44 N CYS B 41 SHEET 1 C 5 LEU C 44 PRO C 49 0 SHEET 2 C 5 TRP C 36 CYS C 41 -1 N THR C 37 O PHE C 48 SHEET 3 C 5 ILE C 24 ARG C 29 -1 N THR C 26 O GLU C 40 SHEET 4 C 5 ALA C 2 ALA C 5 -1 N MET C 3 O ILE C 25 SHEET 5 C 5 CYS C 53 LYS C 54 -1 O LYS C 54 N GLU C 4 SHEET 1 D 5 LEU D 44 PRO D 49 0 SHEET 2 D 5 TRP D 36 CYS D 41 -1 N THR D 37 O PHE D 48 SHEET 3 D 5 ILE D 24 ARG D 29 -1 N THR D 26 O GLU D 40 SHEET 4 D 5 ALA D 2 ALA D 5 -1 N MET D 3 O ILE D 25 SHEET 5 D 5 CYS D 53 LYS D 54 -1 O LYS D 54 N GLU D 4 CRYST1 32.840 51.740 59.940 90.00 89.98 90.00 P 1 21 1 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 0.030451 0.000000 -0.000011 0.00000 SCALE2 0.000000 0.019327 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016683 0.00000