HEADER PROTEIN BINDING 18-AUG-20 7A2J TITLE CRYSTAL STRUCTURE OF THE FYN SH3 DOMAIN IN SPACE GROUP C21 AT PH 7.5 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 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 7A2J 1 REMARK REVDAT 1 25-AUG-21 7A2J 0 JRNL AUTH A.CAMARA-ARTIGAS,M.PLAZA-GARRIDO,M.C.SALINAS-GARCIA JRNL TITL CRYSTAL STRUCTURE OF THE FYN SH3 DOMAIN IN SPACE GROUP C21 JRNL TITL 2 AT PH 7.5 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) : 19.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 22756 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2179 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 19.6300 - 3.7700 0.96 2584 128 0.1512 0.1662 REMARK 3 2 3.7700 - 3.0000 0.96 2585 108 0.1928 0.2324 REMARK 3 3 3.0000 - 2.6200 0.97 2597 126 0.2328 0.2927 REMARK 3 4 2.6200 - 2.3800 0.96 2520 144 0.2412 0.2613 REMARK 3 5 2.3800 - 2.2100 0.97 2600 131 0.2206 0.2719 REMARK 3 6 2.2100 - 2.0800 0.96 2546 145 0.2198 0.2436 REMARK 3 7 2.0800 - 1.9800 0.95 2516 126 0.2293 0.2669 REMARK 3 8 1.9800 - 1.8900 0.94 2535 154 0.2520 0.3642 REMARK 3 9 1.8900 - 1.8200 0.95 2546 138 0.2779 0.2946 REMARK 3 10 1.8200 - 1.7500 0.95 2519 149 0.2883 0.3177 REMARK 3 11 1.7500 - 1.7000 0.96 2520 179 0.3013 0.3731 REMARK 3 12 1.7000 - 1.6500 0.94 2460 134 0.3140 0.2968 REMARK 3 13 1.6500 - 1.6100 0.94 2514 127 0.3243 0.3889 REMARK 3 14 1.6100 - 1.5700 0.93 2512 135 0.3602 0.3638 REMARK 3 15 1.5700 - 1.5300 0.94 2466 155 0.3728 0.3703 REMARK 3 16 1.5300 - 1.5000 0.93 2504 100 0.3987 0.3792 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.790 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.76 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 7A2J 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_1292110708. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.97879 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 : 22756 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 19.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.02800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2000 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 (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.48200 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 (%): 53.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4.5M SODIUM FORMATE, 0.1M HEPES, PH REMARK 280 7.5, 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 36.50550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.37350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 36.50550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.37350 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 HOH A 317 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 241 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 465 GLY B 83 REMARK 465 ASP B 142 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 THR A 85 OG1 CG2 REMARK 470 ARG B 96 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 113 CG OD1 ND2 REMARK 470 SER B 115 OG REMARK 470 GLU B 116 CG CD OE1 OE2 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 ASN B 113 43.70 75.78 REMARK 500 REMARK 500 REMARK: NULL 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 135 O REMARK 620 2 VAL A 138 O 84.9 REMARK 620 3 HOH B 230 O 112.5 70.0 REMARK 620 4 HOH B 234 O 82.2 148.1 88.2 REMARK 620 5 HOH B 235 O 165.6 93.1 80.0 106.1 REMARK 620 N 1 2 3 4 DBREF 7A2J A 83 142 UNP P06241 FYN_HUMAN 83 142 DBREF 7A2J B 83 142 UNP P06241 FYN_HUMAN 83 142 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 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 ALA SEQRES 2 B 60 ARG THR GLU ASP 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 HETNAM NA SODIUM ION FORMUL 3 NA NA 1+ FORMUL 4 HOH *78(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 LEU A 112 O GLU A 121 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 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 O SER A 135 NA NA A 201 1555 1555 2.61 LINK O VAL A 138 NA NA A 201 1555 1555 2.25 LINK NA NA A 201 O HOH B 230 1555 3455 2.99 LINK NA NA A 201 O HOH B 234 1555 3455 2.24 LINK NA NA A 201 O HOH B 235 1555 3455 2.37 CRYST1 73.011 46.747 42.818 90.00 97.84 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 0.013697 0.000000 0.001886 0.00000 SCALE2 0.000000 0.021392 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023575 0.00000