HEADER PROTEIN BINDING 18-AUG-20 7A2Q TITLE CRYSTAL STRUCTURE OF THE FYN SH3 DOMAIN L112V-S114N-S115T-E121L-R123H TITLE 2 MUTANT AT PH 3.0 WITH PEG 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 7A2Q 1 REMARK REVDAT 1 25-AUG-21 7A2Q 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 AT PH 3.0 WITH PEG JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 0.94 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) : 0.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.320 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 36380 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.161 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.150 REMARK 3 FREE R VALUE TEST SET COUNT : 1874 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 28.2100 - 2.2200 0.99 2851 142 0.1711 0.1653 REMARK 3 2 2.2200 - 1.7600 1.00 2708 161 0.1493 0.1373 REMARK 3 3 1.7600 - 1.5400 1.00 2666 170 0.1481 0.1780 REMARK 3 4 1.5400 - 1.4000 1.00 2688 144 0.1411 0.1384 REMARK 3 5 1.4000 - 1.3000 1.00 2676 152 0.1350 0.1865 REMARK 3 6 1.3000 - 1.2200 1.00 2689 128 0.1479 0.1494 REMARK 3 7 1.2200 - 1.1600 1.00 2666 134 0.1367 0.1363 REMARK 3 8 1.1600 - 1.1100 1.00 2620 141 0.1284 0.1531 REMARK 3 9 1.1100 - 1.0700 1.00 2664 136 0.1499 0.1683 REMARK 3 10 1.0700 - 1.0300 0.99 2615 146 0.1890 0.1840 REMARK 3 11 1.0300 - 1.0000 0.99 2595 168 0.2127 0.2424 REMARK 3 12 1.0000 - 0.9700 0.98 2567 133 0.1983 0.2151 REMARK 3 13 0.9700 - 0.9400 0.94 2501 119 0.2496 0.2655 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.380 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.77 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 7A2Q 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_1292110719. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAY-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 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) : 0.979 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 0.6.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36440 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.940 REMARK 200 RESOLUTION RANGE LOW (A) : 32.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.54000 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 (%): 39.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% PEG 300, 5 MM BETA-CYCLODEXTRIN, REMARK 280 2.0 AMMONIUM SULFATE, 0.1M SODIUM CITRATE, PH 5.0, VAPOR REMARK 280 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 14.56000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.78650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.01700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.78650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.56000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 16.01700 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 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 ASP A 142 REMARK 465 SER A 143 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 A 96 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 116 CG CD OE1 OE2 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 474 DISTANCE = 7.00 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 302 DBREF 7A2Q A 83 143 UNP P06241 FYN_HUMAN 83 143 SEQADV 7A2Q VAL A 112 UNP P06241 LEU 112 ENGINEERED MUTATION SEQADV 7A2Q ASN A 114 UNP P06241 SER 114 ENGINEERED MUTATION SEQADV 7A2Q THR A 115 UNP P06241 SER 115 ENGINEERED MUTATION SEQADV 7A2Q LEU A 121 UNP P06241 GLU 121 ENGINEERED MUTATION SEQADV 7A2Q HIS A 123 UNP P06241 ARG 123 ENGINEERED MUTATION SEQRES 1 A 61 GLY VAL THR LEU PHE VAL ALA LEU TYR ASP TYR GLU ALA SEQRES 2 A 61 ARG THR GLU ASP ASP LEU SER PHE HIS LYS GLY GLU LYS SEQRES 3 A 61 PHE GLN ILE VAL ASN ASN THR GLU GLY ASP TRP TRP LEU SEQRES 4 A 61 ALA HIS SER LEU THR THR GLY GLU THR GLY TYR ILE PRO SEQRES 5 A 61 SER ASN TYR VAL ALA PRO VAL ASP SER HET PG4 A 301 31 HET SO4 A 302 5 HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM SO4 SULFATE ION FORMUL 2 PG4 C8 H18 O5 FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *74(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 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 SITE 1 AC1 9 VAL A 84 THR A 85 ASP A 92 GLU A 94 SITE 2 AC1 9 HIS A 104 ILE A 111 VAL A 112 HOH A 441 SITE 3 AC1 9 HOH A 452 SITE 1 AC2 5 SER A 102 THR A 126 HOH A 409 HOH A 426 SITE 2 AC2 5 HOH A 427 CRYST1 29.120 32.034 59.573 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 0.034341 0.000000 0.000000 0.00000 SCALE2 0.000000 0.031217 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016786 0.00000