HEADER PROTEIN BINDING 18-AUG-20 7A2M TITLE CRYSTAL STRUCTURE OF THE FYN SH3 DOMAIN A95S-D99T MUTANT IN C21 SPACE TITLE 2 GROUP COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN KINASE FYN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PROTO-ONCOGENE SYN,PROTO-ONCOGENE C-FYN,SRC-LIKE KINASE,SLK, COMPND 5 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: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: FYN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PHTP1 KEYWDS BETA BARREL, SH3 DOMAIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR A.CAMARA-ARTIGAS,M.PLAZA-GARRIDO,M.C.SALINAS-GARCIA REVDAT 2 31-JAN-24 7A2M 1 REMARK REVDAT 1 25-AUG-21 7A2M 0 JRNL AUTH A.CAMARA-ARTIGAS,M.PLAZA-GARRIDO,M.C.SALINAS-GARCIA JRNL TITL CRYSTAL STRUCTURE OF THE FYN SH3 DOMAIN A95S-D99T MUTANT IN JRNL TITL 2 C21 SPACE GROUP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2-3874 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.910 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.3 REMARK 3 NUMBER OF REFLECTIONS : 37874 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 1863 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.7000 - 3.5200 0.88 2884 176 0.1551 0.1878 REMARK 3 2 3.5200 - 2.8000 0.90 2967 141 0.1880 0.2603 REMARK 3 3 2.8000 - 2.4400 0.90 2946 156 0.2358 0.2915 REMARK 3 4 2.4400 - 2.2200 0.89 2931 150 0.2276 0.2762 REMARK 3 5 2.2200 - 2.0600 0.87 2852 123 0.2223 0.2469 REMARK 3 6 2.0600 - 1.9400 0.85 2817 118 0.2377 0.2621 REMARK 3 7 1.9400 - 1.8400 0.85 2807 140 0.2721 0.3265 REMARK 3 8 1.8400 - 1.7600 0.84 2735 161 0.2812 0.2862 REMARK 3 9 1.7600 - 1.7000 0.84 2739 167 0.3071 0.3287 REMARK 3 10 1.7000 - 1.6400 0.85 2769 140 0.3228 0.3882 REMARK 3 11 1.6400 - 1.5900 0.85 2769 142 0.3528 0.3884 REMARK 3 12 1.5900 - 1.5400 0.79 2625 131 0.3813 0.3912 REMARK 3 13 1.5400 - 1.5000 0.66 2170 118 0.4002 0.4390 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.18 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7A2M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1292110713. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-FEB-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID30B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976251 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37874 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 19.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.63800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3UA6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4.5 M SODIUM FORMATE, 0.1 SODIUM REMARK 280 ACETATE, PH 4.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 36.34700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.52400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 36.34700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.52400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 S SO4 A 203 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 348 LIES ON A SPECIAL POSITION. 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 GLY A 83 REMARK 465 VAL A 84 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 ARG B 96 CG CD NE CZ NH1 NH2 REMARK 470 THR B 97 OG1 CG2 REMARK 470 GLU B 98 CG CD OE1 OE2 REMARK 470 GLU B 116 CG CD OE1 OE2 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 201 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 95 OG REMARK 620 2 THR A 97 O 98.8 REMARK 620 3 ASP A 100 O 88.5 88.5 REMARK 620 4 HOH A 321 O 140.5 118.5 80.4 REMARK 620 5 HOH A 325 O 88.0 84.0 171.1 107.3 REMARK 620 6 HOH A 330 O 80.0 171.1 100.2 65.1 87.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 135 O REMARK 620 2 VAL A 138 O 86.5 REMARK 620 3 HOH B 326 O 85.8 172.1 REMARK 620 4 HOH B 332 O 140.3 92.7 92.3 REMARK 620 5 HOH B 333 O 125.3 87.5 98.1 94.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 201 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 135 O REMARK 620 2 VAL B 138 O 71.2 REMARK 620 3 HOH B 336 O 90.9 63.3 REMARK 620 4 HOH B 338 O 133.8 75.7 102.2 REMARK 620 N 1 2 3 DBREF 7A2M A 83 142 UNP P06241 FYN_HUMAN 83 142 DBREF 7A2M B 83 142 UNP P06241 FYN_HUMAN 83 142 SEQADV 7A2M SER A 95 UNP P06241 ALA 95 ENGINEERED MUTATION SEQADV 7A2M THR A 99 UNP P06241 ASP 99 ENGINEERED MUTATION SEQADV 7A2M SER B 95 UNP P06241 ALA 95 ENGINEERED MUTATION SEQADV 7A2M THR B 99 UNP P06241 ASP 99 ENGINEERED MUTATION SEQRES 1 A 60 GLY VAL THR LEU PHE VAL ALA LEU TYR ASP TYR GLU SER SEQRES 2 A 60 ARG THR GLU THR ASP LEU SER PHE HIS LYS GLY GLU LYS SEQRES 3 A 60 PHE GLN ILE LEU ASN SER SER GLU GLY ASP TRP TRP GLU SEQRES 4 A 60 ALA ARG SER LEU THR THR GLY GLU THR GLY TYR ILE PRO SEQRES 5 A 60 SER ASN TYR VAL ALA PRO VAL ASP SEQRES 1 B 60 GLY VAL THR LEU PHE VAL ALA LEU TYR ASP TYR GLU SER SEQRES 2 B 60 ARG THR GLU THR ASP LEU SER PHE HIS LYS GLY GLU LYS SEQRES 3 B 60 PHE GLN ILE LEU ASN SER SER GLU GLY ASP TRP TRP GLU SEQRES 4 B 60 ALA ARG SER LEU THR THR GLY GLU THR GLY TYR ILE PRO SEQRES 5 B 60 SER ASN TYR VAL ALA PRO VAL ASP HET NA A 201 1 HET NA A 202 1 HET SO4 A 203 5 HET NA B 201 1 HET FMT B 202 5 HETNAM NA SODIUM ION HETNAM SO4 SULFATE ION HETNAM FMT FORMIC ACID FORMUL 3 NA 3(NA 1+) FORMUL 5 SO4 O4 S 2- FORMUL 7 FMT C H2 O2 FORMUL 8 HOH *91(H2 O) SHEET 1 AA1 5 THR A 130 PRO A 134 0 SHEET 2 AA1 5 TRP A 119 SER A 124 -1 N TRP A 120 O ILE A 133 SHEET 3 AA1 5 LYS A 108 ASN A 113 -1 N LEU A 112 O GLU A 121 SHEET 4 AA1 5 LEU A 86 ALA A 89 -1 N PHE A 87 O PHE A 109 SHEET 5 AA1 5 VAL A 138 PRO A 140 -1 O ALA A 139 N VAL A 88 SHEET 1 AA2 5 THR B 130 PRO B 134 0 SHEET 2 AA2 5 TRP B 119 SER B 124 -1 N ALA B 122 O GLY B 131 SHEET 3 AA2 5 LYS B 108 GLN B 110 -1 N GLN B 110 O ARG B 123 SHEET 4 AA2 5 LEU B 86 ALA B 89 -1 N PHE B 87 O PHE B 109 SHEET 5 AA2 5 VAL B 138 PRO B 140 -1 O ALA B 139 N VAL B 88 LINK OG SER A 95 NA NA A 201 1555 1555 2.41 LINK O THR A 97 NA NA A 201 1555 1555 2.31 LINK O ASP A 100 NA NA A 201 1555 1555 2.28 LINK O SER A 135 NA NA A 202 1555 1555 2.57 LINK O VAL A 138 NA NA A 202 1555 1555 2.13 LINK NA NA A 201 O HOH A 321 1555 1555 2.34 LINK NA NA A 201 O HOH A 325 1555 1555 2.28 LINK NA NA A 201 O HOH A 330 1555 1555 2.93 LINK NA NA A 202 O HOH B 326 1555 3455 2.33 LINK NA NA A 202 O HOH B 332 1555 3455 2.46 LINK NA NA A 202 O HOH B 333 1555 3455 2.36 LINK O SER B 135 NA NA B 201 1555 1555 2.58 LINK O VAL B 138 NA NA B 201 1555 1555 3.05 LINK NA NA B 201 O HOH B 336 1555 1555 2.76 LINK NA NA B 201 O HOH B 338 1555 1555 2.37 CRYST1 72.694 47.048 42.712 90.00 97.42 90.00 C 1 2 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 0.013756 0.000000 0.001792 0.00000 SCALE2 0.000000 0.021255 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023610 0.00000