HEADER PROTEIN BINDING 18-AUG-20 7A2U TITLE CRYSTAL STRUCTURE OF THE FYN SH3 DOMAIN L112V-S114N-S115T AT PH 4.5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN KINASE FYN; COMPND 3 CHAIN: A; 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 7A2U 1 REMARK REVDAT 1 25-AUG-21 7A2U 0 JRNL AUTH A.CAMARA-ARTIGAS,M.PLAZA-GARRIDO,M.C.SALINAS-GARCIA JRNL TITL CRYSTAL STRUCTURE OF THE FYN SH3 DOMAIN L112V-S114N-S115T AT JRNL TITL 2 PH 4.5 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_3951 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 14722 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 732 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 19.9400 - 2.9100 1.00 2913 143 0.1308 0.1683 REMARK 3 2 2.9100 - 2.3100 1.00 2887 176 0.1715 0.2193 REMARK 3 3 2.3100 - 2.0200 0.98 2876 139 0.1749 0.2175 REMARK 3 4 2.0200 - 1.8300 0.97 2796 183 0.2023 0.2190 REMARK 3 5 1.8300 - 1.7000 0.85 2518 91 0.2734 0.3035 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) : 0.101 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.051 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.57 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 : 0.019 490 REMARK 3 ANGLE : 1.389 670 REMARK 3 CHIRALITY : 0.088 72 REMARK 3 PLANARITY : 0.012 88 REMARK 3 DIHEDRAL : 12.593 163 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 108 THROUGH 118 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.5866 2.0384 -3.7721 REMARK 3 T TENSOR REMARK 3 T11: 0.2354 T22: 0.3260 REMARK 3 T33: 0.2665 T12: 0.0010 REMARK 3 T13: 0.0104 T23: 0.0523 REMARK 3 L TENSOR REMARK 3 L11: 5.8631 L22: 5.0779 REMARK 3 L33: 4.5905 L12: 3.9658 REMARK 3 L13: -3.0176 L23: -4.0630 REMARK 3 S TENSOR REMARK 3 S11: -0.1911 S12: 0.1528 S13: -0.1639 REMARK 3 S21: 0.0471 S22: 0.3801 S23: 0.5294 REMARK 3 S31: 0.3250 S32: -1.1349 S33: -0.3478 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 119 THROUGH 129 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.7789 3.1078 -6.1640 REMARK 3 T TENSOR REMARK 3 T11: 0.1487 T22: 0.1075 REMARK 3 T33: 0.1314 T12: 0.0050 REMARK 3 T13: -0.0151 T23: -0.0193 REMARK 3 L TENSOR REMARK 3 L11: 7.4289 L22: 3.0421 REMARK 3 L33: 6.7675 L12: 1.8369 REMARK 3 L13: -5.4710 L23: -2.3355 REMARK 3 S TENSOR REMARK 3 S11: -0.1561 S12: 0.2874 S13: -0.2494 REMARK 3 S21: -0.2315 S22: 0.1338 S23: -0.0987 REMARK 3 S31: 0.2879 S32: -0.1614 S33: -0.0071 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 130 THROUGH 142 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.5821 8.0710 -2.3523 REMARK 3 T TENSOR REMARK 3 T11: 0.0877 T22: 0.1561 REMARK 3 T33: 0.0851 T12: 0.0007 REMARK 3 T13: 0.0111 T23: 0.0135 REMARK 3 L TENSOR REMARK 3 L11: 3.6801 L22: 5.3429 REMARK 3 L33: 1.7431 L12: -2.6319 REMARK 3 L13: 1.0340 L23: -1.1928 REMARK 3 S TENSOR REMARK 3 S11: 0.0773 S12: 0.0091 S13: -0.0002 REMARK 3 S21: -0.2133 S22: 0.0101 S23: 0.1186 REMARK 3 S31: -0.0260 S32: -0.2533 S33: -0.0958 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 83 THROUGH 94 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.3491 11.1328 -4.0349 REMARK 3 T TENSOR REMARK 3 T11: 0.1425 T22: 0.2008 REMARK 3 T33: 0.1442 T12: 0.0261 REMARK 3 T13: 0.0591 T23: -0.0055 REMARK 3 L TENSOR REMARK 3 L11: 6.0248 L22: 3.0576 REMARK 3 L33: 7.6585 L12: 2.4013 REMARK 3 L13: 6.2400 L23: 1.7126 REMARK 3 S TENSOR REMARK 3 S11: -0.1284 S12: 0.0520 S13: 0.0959 REMARK 3 S21: -0.1124 S22: 0.0320 S23: 0.0019 REMARK 3 S31: -0.2827 S32: -0.0373 S33: 0.0784 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 95 THROUGH 107 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.9115 6.9222 -0.9797 REMARK 3 T TENSOR REMARK 3 T11: 0.1143 T22: 0.1509 REMARK 3 T33: 0.1421 T12: 0.0185 REMARK 3 T13: 0.0150 T23: -0.0470 REMARK 3 L TENSOR REMARK 3 L11: 2.7153 L22: 8.7969 REMARK 3 L33: 8.2218 L12: 1.0529 REMARK 3 L13: 0.6342 L23: -5.6026 REMARK 3 S TENSOR REMARK 3 S11: -0.0383 S12: -0.0875 S13: -0.0886 REMARK 3 S21: 0.2724 S22: -0.0156 S23: -0.5069 REMARK 3 S31: -0.0224 S32: 0.2412 S33: 0.0294 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 7A2U 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_1292110725. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97910 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14723 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 19.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9000 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 (%) : 88.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.49700 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 (%): 53.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M AMMONIUM SULFATE, 0.1 SODIUM REMARK 280 ACETATE, PH 4.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 19.63267 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 39.26533 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.44900 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.08167 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 9.81633 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL 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 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 94 CG CD OE1 OE2 REMARK 470 ARG A 96 CG CD NE CZ NH1 NH2 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 GLU A 116 -115.38 -98.51 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 ACT A 201 DBREF 7A2U A 83 142 UNP P06241 FYN_HUMAN 83 142 SEQADV 7A2U VAL A 112 UNP P06241 LEU 112 ENGINEERED MUTATION SEQADV 7A2U ASN A 114 UNP P06241 SER 114 ENGINEERED MUTATION SEQADV 7A2U THR A 115 UNP P06241 SER 115 ENGINEERED MUTATION SEQRES 1 A 60 GLY VAL THR LEU PHE VAL ALA LEU TYR ASP TYR GLU ALA SEQRES 2 A 60 ARG THR GLU ASP ASP LEU SER PHE HIS LYS GLY GLU LYS SEQRES 3 A 60 PHE GLN ILE VAL ASN ASN THR 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 HET ACT A 201 7 HETNAM ACT ACETATE ION FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 HOH *55(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 ALA A 122 O GLY A 131 SHEET 3 AA1 5 LYS A 108 ASN A 113 -1 N GLN A 110 O ARG A 123 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 SITE 1 AC1 4 THR A 97 GLU A 98 SER A 102 HOH A 319 CRYST1 46.039 46.039 58.898 90.00 90.00 120.00 P 61 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 0.021721 0.012540 0.000000 0.00000 SCALE2 0.000000 0.025081 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016979 0.00000