HEADER PROTEIN BINDING 18-AUG-20 7A2W TITLE CRYSTAL STRUCTURE OF THE FYN SH3 DOMAIN L112V-S114N-S115T-E121L-R123H TITLE 2 MUTANT IN COMPLEX WITH VSL12 AT PH 3.0 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN KINASE FYN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SH3 DOMAIN; COMPND 5 SYNONYM: PROTO-ONCOGENE SYN,PROTO-ONCOGENE C-FYN,SRC-LIKE KINASE,SLK, COMPND 6 P59-FYN; COMPND 7 EC: 2.7.10.2; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: VSL12; COMPND 12 CHAIN: B; COMPND 13 FRAGMENT: VSL12; COMPND 14 ENGINEERED: 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; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS BETA BARREL, SH3 DOMAIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR A.CAMARA-ARTIGAS,M.PLAZA-GARRIDO,M.C.SALINAS-GARCIA REVDAT 3 23-OCT-24 7A2W 1 REMARK REVDAT 2 31-JAN-24 7A2W 1 REMARK REVDAT 1 25-AUG-21 7A2W 0 JRNL AUTH A.CAMARA-ARTIGAS,M.PLAZA-GARRIDO,M.C.SALINAS-GARCIA JRNL TITL CRYSTAL STRUCTURE OF THE FYN SH3 DOMAIN JRNL TITL 2 L112V-S114N-S115T-E121L-R123H MUTANT IN COMPLEX WITH VSL12 JRNL TITL 3 AT PH 3.0 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 0.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1-3660 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) : 0.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.160 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 71263 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.132 REMARK 3 R VALUE (WORKING SET) : 0.131 REMARK 3 FREE R VALUE : 0.152 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850 REMARK 3 FREE R VALUE TEST SET COUNT : 3454 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 18.6900 - 2.8900 0.93 2594 151 0.1395 0.1912 REMARK 3 2 2.8900 - 2.3000 0.92 2554 119 0.1564 0.1280 REMARK 3 3 2.3000 - 2.0100 0.80 2242 119 0.1335 0.1375 REMARK 3 4 2.0100 - 1.8200 0.86 2374 118 0.1241 0.1471 REMARK 3 5 1.8200 - 1.6900 0.97 2746 133 0.1244 0.1519 REMARK 3 6 1.6900 - 1.5900 0.99 2754 159 0.1096 0.1238 REMARK 3 7 1.5900 - 1.5100 0.99 2761 148 0.1109 0.1362 REMARK 3 8 1.5100 - 1.4500 1.00 2729 148 0.1075 0.1434 REMARK 3 9 1.4500 - 1.3900 0.99 2796 162 0.1125 0.1372 REMARK 3 10 1.3900 - 1.3400 1.00 2764 159 0.1164 0.1398 REMARK 3 11 1.3400 - 1.3000 1.00 2744 184 0.1101 0.1399 REMARK 3 12 1.3000 - 1.2600 1.00 2763 124 0.1129 0.1263 REMARK 3 13 1.2600 - 1.2300 1.00 2853 127 0.1134 0.1096 REMARK 3 14 1.2300 - 1.2000 0.99 2781 133 0.1110 0.1447 REMARK 3 15 1.2000 - 1.1700 1.00 2759 164 0.1149 0.1237 REMARK 3 16 1.1700 - 1.1500 0.99 2734 153 0.1125 0.1278 REMARK 3 17 1.1500 - 1.1300 1.00 2791 110 0.1214 0.1341 REMARK 3 18 1.1300 - 1.1000 1.00 2857 117 0.1186 0.1356 REMARK 3 19 1.1000 - 1.0800 0.99 2775 125 0.1287 0.1393 REMARK 3 20 1.0800 - 1.0700 0.99 2766 119 0.1406 0.1524 REMARK 3 21 1.0700 - 1.0500 0.99 2794 133 0.1520 0.1631 REMARK 3 22 1.0500 - 1.0300 0.98 2723 142 0.1655 0.2386 REMARK 3 23 1.0300 - 1.0200 0.98 2752 123 0.1854 0.2567 REMARK 3 24 1.0200 - 1.0000 0.99 2772 181 0.1994 0.2255 REMARK 3 25 1.0000 - 0.9900 0.95 2631 103 0.2250 0.2124 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.390 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.37 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 7A2W 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_1292110728. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-SEP-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.0 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) : 0.9792 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 0.5.31 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 71263 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.990 REMARK 200 RESOLUTION RANGE LOW (A) : 18.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.90 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 13.50 REMARK 200 R MERGE FOR SHELL (I) : 0.52500 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 (%): 40.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 M AMMONIUM SULFATE, 0.1 SODIUM REMARK 280 CITRATE, PH 3.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 16.45250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.39800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.44200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.39800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.45250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 16.44200 REMARK 290 SMTRY3 4 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: 1370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 DBREF 7A2W A 83 142 UNP P06241 FYN_HUMAN 83 142 DBREF 7A2W B 0 12 PDB 7A2W 7A2W 0 12 SEQADV 7A2W GLY A 82 UNP P06241 EXPRESSION TAG SEQADV 7A2W VAL A 112 UNP P06241 LEU 112 ENGINEERED MUTATION SEQADV 7A2W ASN A 114 UNP P06241 SER 114 ENGINEERED MUTATION SEQADV 7A2W THR A 115 UNP P06241 SER 115 ENGINEERED MUTATION SEQADV 7A2W LEU A 121 UNP P06241 GLU 121 ENGINEERED MUTATION SEQADV 7A2W HIS A 123 UNP P06241 ARG 123 ENGINEERED MUTATION SEQRES 1 A 61 GLY GLY VAL THR LEU PHE VAL ALA LEU TYR ASP TYR GLU SEQRES 2 A 61 ALA ARG THR GLU ASP ASP LEU SER PHE HIS LYS GLY GLU SEQRES 3 A 61 LYS PHE GLN ILE VAL ASN ASN THR GLU GLY ASP TRP TRP SEQRES 4 A 61 LEU ALA HIS SER LEU THR THR GLY GLU THR GLY TYR ILE SEQRES 5 A 61 PRO SER ASN TYR VAL ALA PRO VAL ASP SEQRES 1 B 13 ACE VAL SER LEU ALA ARG ARG PRO LEU PRO PRO LEU PRO HET ACE B 0 6 HET CIT B 101 18 HETNAM ACE ACETYL GROUP HETNAM CIT CITRIC ACID FORMUL 2 ACE C2 H4 O FORMUL 3 CIT C6 H8 O7 FORMUL 4 HOH *119(H2 O) HELIX 1 AA1 SER B 2 ARG B 6 5 5 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 HIS A 123 SHEET 4 AA1 5 PHE A 87 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 LINK C ACE B 0 N VAL B 1 1555 1555 1.42 CRYST1 32.905 32.884 62.796 90.00 90.00 90.00 P 21 21 21 4 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 0.030391 0.000000 0.000000 0.00000 SCALE2 0.000000 0.030410 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015925 0.00000