HEADER TRANSFERASE 03-APR-08 3CQT TITLE N53I V55L MUTANT OF FYN SH3 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE FYN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FYN SH3 DOMAIN; COMPND 5 SYNONYM: P59-FYN; COMPND 6 EC: 2.7.10.2; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_STRAIN: BL21*; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PET21D(+) KEYWDS BETA BARREL, ATP-BINDING, DEVELOPMENTAL PROTEIN, KINASE, LIPOPROTEIN, KEYWDS 2 MANGANESE, METAL-BINDING, MYRISTATE, NUCLEOTIDE-BINDING, PALMITATE, KEYWDS 3 PHOSPHOPROTEIN, PROTO-ONCOGENE, SH2 DOMAIN, SH3 DOMAIN, TRANSFERASE, KEYWDS 4 TYROSINE-PROTEIN KINASE EXPDTA X-RAY DIFFRACTION AUTHOR A.M.NECULAI,A.ZARRINE-AFSAR,P.L.HOWELL,A.DAVIDSON,H.S.CHAN REVDAT 3 20-OCT-21 3CQT 1 SEQADV REVDAT 2 24-FEB-09 3CQT 1 VERSN REVDAT 1 01-JUL-08 3CQT 0 JRNL AUTH A.ZARRINE-AFSAR,S.WALLIN,A.M.NECULAI,P.NEUDECKER,P.L.HOWELL, JRNL AUTH 2 A.R.DAVIDSON,H.S.CHAN JRNL TITL THEORETICAL AND EXPERIMENTAL DEMONSTRATION OF THE IMPORTANCE JRNL TITL 2 OF SPECIFIC NONNATIVE INTERACTIONS IN PROTEIN FOLDING. JRNL REF PROC.NATL.ACAD.SCI.USA V. 105 9999 2008 JRNL REFN ISSN 0027-8424 JRNL PMID 18626019 JRNL DOI 10.1073/PNAS.0801874105 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0036 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.06 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 8516 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 + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 435 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 625 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE SET COUNT : 37 REMARK 3 BIN FREE R VALUE : 0.2460 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 471 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 89 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.22000 REMARK 3 B22 (A**2) : -0.22000 REMARK 3 B33 (A**2) : 0.33000 REMARK 3 B12 (A**2) : -0.11000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.106 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.103 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.055 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.464 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 513 ; 0.006 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 702 ; 0.971 ; 1.934 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 63 ; 6.042 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 27 ;29.660 ;24.444 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 79 ;12.883 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 2 ;25.935 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 72 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 411 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 209 ; 0.179 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 351 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 64 ; 0.088 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 37 ; 0.202 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.095 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 312 ; 0.554 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 493 ; 0.971 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 237 ; 1.305 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 209 ; 1.896 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3CQT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-APR-08. REMARK 100 THE DEPOSITION ID IS D_1000047101. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUL-07 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 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 RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NI MIRROR 0.3 + NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8962 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 45.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.07280 REMARK 200 R SYM (I) : 0.01750 REMARK 200 FOR THE DATA SET : 53.0700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.11780 REMARK 200 R SYM FOR SHELL (I) : 0.03100 REMARK 200 FOR SHELL : 33.05 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: COMO REMARK 200 STARTING MODEL: PDB ENTRY 1FYN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CACODYLATE, 1.4 M SODIUM REMARK 280 ACETATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 14.93900 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 29.87800 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 29.87800 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 14.93900 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 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 -3 REMARK 465 VAL A -2 REMARK 465 GLN A -1 REMARK 465 ILE A 0 REMARK 465 ASP A 59 REMARK 465 ARG A 60 REMARK 465 LEU A 61 REMARK 465 ASP A 62 REMARK 465 TYR A 63 REMARK 465 LYS A 64 REMARK 465 ASP A 65 REMARK 465 ASP A 66 REMARK 465 ASP A 67 REMARK 465 ASP A 68 REMARK 465 LYS A 69 REMARK 465 HIS A 70 REMARK 465 HIS A 71 REMARK 465 HIS A 72 REMARK 465 HIS A 73 REMARK 465 HIS A 74 REMARK 465 HIS A 75 DBREF 3CQT A 2 59 UNP Q05876 FYN_CHICK 85 142 SEQADV 3CQT MET A -3 UNP Q05876 EXPRESSION TAG SEQADV 3CQT VAL A -2 UNP Q05876 EXPRESSION TAG SEQADV 3CQT GLN A -1 UNP Q05876 EXPRESSION TAG SEQADV 3CQT ILE A 0 UNP Q05876 EXPRESSION TAG SEQADV 3CQT SER A 1 UNP Q05876 EXPRESSION TAG SEQADV 3CQT ILE A 53 UNP Q05876 ASN 136 ENGINEERED MUTATION SEQADV 3CQT LEU A 55 UNP Q05876 VAL 138 ENGINEERED MUTATION SEQADV 3CQT ARG A 60 UNP Q05876 EXPRESSION TAG SEQADV 3CQT LEU A 61 UNP Q05876 EXPRESSION TAG SEQADV 3CQT ASP A 62 UNP Q05876 EXPRESSION TAG SEQADV 3CQT TYR A 63 UNP Q05876 EXPRESSION TAG SEQADV 3CQT LYS A 64 UNP Q05876 EXPRESSION TAG SEQADV 3CQT ASP A 65 UNP Q05876 EXPRESSION TAG SEQADV 3CQT ASP A 66 UNP Q05876 EXPRESSION TAG SEQADV 3CQT ASP A 67 UNP Q05876 EXPRESSION TAG SEQADV 3CQT ASP A 68 UNP Q05876 EXPRESSION TAG SEQADV 3CQT LYS A 69 UNP Q05876 EXPRESSION TAG SEQADV 3CQT HIS A 70 UNP Q05876 EXPRESSION TAG SEQADV 3CQT HIS A 71 UNP Q05876 EXPRESSION TAG SEQADV 3CQT HIS A 72 UNP Q05876 EXPRESSION TAG SEQADV 3CQT HIS A 73 UNP Q05876 EXPRESSION TAG SEQADV 3CQT HIS A 74 UNP Q05876 EXPRESSION TAG SEQADV 3CQT HIS A 75 UNP Q05876 EXPRESSION TAG SEQRES 1 A 79 MET VAL GLN ILE SER THR LEU PHE GLU ALA LEU TYR ASP SEQRES 2 A 79 TYR GLU ALA ARG THR GLU ASP ASP LEU SER PHE HIS LYS SEQRES 3 A 79 GLY GLU LYS PHE GLN ILE LEU ASN SER SER GLU GLY ASP SEQRES 4 A 79 TRP TRP GLU ALA ARG SER LEU THR THR GLY GLU THR GLY SEQRES 5 A 79 TYR ILE PRO SER ILE TYR LEU ALA PRO VAL ASP ARG LEU SEQRES 6 A 79 ASP TYR LYS ASP ASP ASP ASP LYS HIS HIS HIS HIS HIS SEQRES 7 A 79 HIS FORMUL 2 HOH *89(H2 O) SHEET 1 A 5 THR A 47 PRO A 51 0 SHEET 2 A 5 TRP A 36 SER A 41 -1 N ALA A 39 O GLY A 48 SHEET 3 A 5 LYS A 25 ASN A 30 -1 N GLN A 27 O ARG A 40 SHEET 4 A 5 PHE A 4 ALA A 6 -1 N PHE A 4 O PHE A 26 SHEET 5 A 5 LEU A 55 PRO A 57 -1 O ALA A 56 N GLU A 5 CRYST1 52.032 52.032 44.817 90.00 90.00 120.00 P 31 2 1 6 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 0.019219 0.011096 0.000000 0.00000 SCALE2 0.000000 0.022192 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022313 0.00000