HEADER PROTEIN BINDING 05-OCT-21 7PVW TITLE CRYSTAL STRUCTURE OF THE INTERTWINED DIMER OF THE C-SRC SH3 DOMAIN TITLE 2 E93V-S94A-R95S-T96G-N112G-N113Y-T114N-E115H MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOFORM 1 OF PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PROTO-ONCOGENE C-SRC,PP60C-SRC,P60-SRC; COMPND 5 EC: 2.7.10.2; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 GENE: SRC; 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.C.SALINAS GARCIA REVDAT 3 10-SEP-25 7PVW 1 JRNL REVDAT 2 31-JAN-24 7PVW 1 REMARK REVDAT 1 14-SEP-22 7PVW 0 JRNL AUTH M.C.SALINAS-GARCIA,M.PLAZA-GARRIDO,J.C.MARTINEZ, JRNL AUTH 2 A.CAMARA-ARTIGAS JRNL TITL UNDERSTANDING DOMAIN SWAPPING IN THE C-SRC SH3 DOMAIN JRNL TITL 2 THROUGH HINGE-LOOP MUTAGENESIS. JRNL REF ACTA CRYSTALLOGR D STRUCT 2025 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 40862305 JRNL DOI 10.1107/S2059798325006977 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1 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) : 19.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.150 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 38058 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1939 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 19.6400 - 3.6100 1.00 2584 138 0.1397 0.1592 REMARK 3 2 3.6100 - 2.8700 0.99 2581 131 0.1510 0.1954 REMARK 3 3 2.8700 - 2.5100 1.00 2571 168 0.1847 0.1966 REMARK 3 4 2.5100 - 2.2800 1.00 2599 114 0.1746 0.1931 REMARK 3 5 2.2800 - 2.1100 1.00 2580 120 0.1698 0.2032 REMARK 3 6 2.1100 - 1.9900 1.00 2623 134 0.1616 0.1735 REMARK 3 7 1.9900 - 1.8900 1.00 2569 140 0.1866 0.2209 REMARK 3 8 1.8900 - 1.8100 0.99 2594 150 0.1319 0.1760 REMARK 3 9 1.8100 - 1.7400 0.99 2514 177 0.1530 0.2306 REMARK 3 10 1.7400 - 1.6800 0.99 2567 138 0.1911 0.2412 REMARK 3 11 1.6800 - 1.6300 0.99 2598 118 0.1923 0.2040 REMARK 3 12 1.6300 - 1.5800 0.99 2583 111 0.1893 0.2086 REMARK 3 13 1.5800 - 1.5400 0.99 2616 138 0.2112 0.2747 REMARK 3 14 1.5400 - 1.5000 0.99 2540 162 0.2311 0.2545 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.90 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 7PVW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-OCT-21. REMARK 100 THE DEPOSITION ID IS D_1292118460. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAR-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 : 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) : 0.97926 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 : 19622 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 19.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.9000 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 1.00800 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: 4LE9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.9 M AMMONIUM SULFATE, 0.1M 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: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 0.00000 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 0.00000 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 23.09150 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 23.09150 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 23.09150 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: 5400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 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 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 ASP A 141 DBREF 7PVW A 82 141 UNP P00523-1 SRC-1_CHICK 82 141 DBREF 7PVW B 82 141 UNP P00523-1 SRC-1_CHICK 82 141 SEQADV 7PVW VAL A 93 UNP P00523-1 GLU 93 ENGINEERED MUTATION SEQADV 7PVW ALA A 94 UNP P00523-1 SER 94 ENGINEERED MUTATION SEQADV 7PVW SER A 95 UNP P00523-1 ARG 95 ENGINEERED MUTATION SEQADV 7PVW GLY A 96 UNP P00523-1 THR 96 ENGINEERED MUTATION SEQADV 7PVW GLY A 112 UNP P00523-1 ASN 112 ENGINEERED MUTATION SEQADV 7PVW TYR A 113 UNP P00523-1 ASN 113 ENGINEERED MUTATION SEQADV 7PVW ASN A 114 UNP P00523-1 THR 114 ENGINEERED MUTATION SEQADV 7PVW HIS A 115 UNP P00523-1 GLU 115 ENGINEERED MUTATION SEQADV 7PVW VAL B 93 UNP P00523-1 GLU 93 ENGINEERED MUTATION SEQADV 7PVW ALA B 94 UNP P00523-1 SER 94 ENGINEERED MUTATION SEQADV 7PVW SER B 95 UNP P00523-1 ARG 95 ENGINEERED MUTATION SEQADV 7PVW GLY B 96 UNP P00523-1 THR 96 ENGINEERED MUTATION SEQADV 7PVW GLY B 112 UNP P00523-1 ASN 112 ENGINEERED MUTATION SEQADV 7PVW TYR B 113 UNP P00523-1 ASN 113 ENGINEERED MUTATION SEQADV 7PVW ASN B 114 UNP P00523-1 THR 114 ENGINEERED MUTATION SEQADV 7PVW HIS B 115 UNP P00523-1 GLU 115 ENGINEERED MUTATION SEQRES 1 A 60 GLY VAL THR THR PHE VAL ALA LEU TYR ASP TYR VAL ALA SEQRES 2 A 60 SER GLY GLU THR ASP LEU SER PHE LYS LYS GLY GLU ARG SEQRES 3 A 60 LEU GLN ILE VAL GLY TYR ASN HIS GLY ASP TRP TRP LEU SEQRES 4 A 60 ALA HIS SER LEU THR THR GLY GLN THR GLY TYR ILE PRO SEQRES 5 A 60 SER ASN TYR VAL ALA PRO SER ASP SEQRES 1 B 60 GLY VAL THR THR PHE VAL ALA LEU TYR ASP TYR VAL ALA SEQRES 2 B 60 SER GLY GLU THR ASP LEU SER PHE LYS LYS GLY GLU ARG SEQRES 3 B 60 LEU GLN ILE VAL GLY TYR ASN HIS GLY ASP TRP TRP LEU SEQRES 4 B 60 ALA HIS SER LEU THR THR GLY GLN THR GLY TYR ILE PRO SEQRES 5 B 60 SER ASN TYR VAL ALA PRO SER ASP HET PG4 A 201 31 HET ACT A 202 7 HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM ACT ACETATE ION FORMUL 3 PG4 C8 H18 O5 FORMUL 4 ACT C2 H3 O2 1- FORMUL 5 HOH *85(H2 O) HELIX 1 AA1 GLY A 112 GLY A 116 5 5 HELIX 2 AA2 GLY B 112 GLY B 116 5 5 SHEET 1 AA1 5 THR A 129 PRO A 133 0 SHEET 2 AA1 5 TRP A 118 SER A 123 -1 N TRP A 119 O ILE A 132 SHEET 3 AA1 5 ARG B 107 ILE B 110 -1 O GLN B 109 N HIS A 122 SHEET 4 AA1 5 THR A 85 ALA A 88 -1 N PHE A 86 O LEU B 108 SHEET 5 AA1 5 VAL A 137 SER A 140 -1 O ALA A 138 N VAL A 87 SHEET 1 AA2 5 THR B 129 PRO B 133 0 SHEET 2 AA2 5 TRP B 118 SER B 123 -1 N TRP B 119 O ILE B 132 SHEET 3 AA2 5 ARG A 107 ILE A 110 -1 N GLN A 109 O HIS B 122 SHEET 4 AA2 5 PHE B 86 ALA B 88 -1 O PHE B 86 N LEU A 108 SHEET 5 AA2 5 VAL B 137 PRO B 139 -1 O ALA B 138 N VAL B 87 CRYST1 68.037 68.037 46.183 90.00 90.00 120.00 P 63 12 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 0.014698 0.008486 0.000000 0.00000 SCALE2 0.000000 0.016972 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021653 0.00000 CONECT 1810 1811 1823 CONECT 1811 1810 1812 1824 1825 CONECT 1812 1811 1813 1826 1827 CONECT 1813 1812 1814 CONECT 1814 1813 1815 1828 1829 CONECT 1815 1814 1816 1830 1831 CONECT 1816 1815 1817 CONECT 1817 1816 1818 1832 1833 CONECT 1818 1817 1819 1834 1835 CONECT 1819 1818 1820 CONECT 1820 1819 1821 1836 1837 CONECT 1821 1820 1822 1838 1839 CONECT 1822 1821 1840 CONECT 1823 1810 CONECT 1824 1811 CONECT 1825 1811 CONECT 1826 1812 CONECT 1827 1812 CONECT 1828 1814 CONECT 1829 1814 CONECT 1830 1815 CONECT 1831 1815 CONECT 1832 1817 CONECT 1833 1817 CONECT 1834 1818 CONECT 1835 1818 CONECT 1836 1820 CONECT 1837 1820 CONECT 1838 1821 CONECT 1839 1821 CONECT 1840 1822 CONECT 1841 1842 1843 1844 CONECT 1842 1841 CONECT 1843 1841 CONECT 1844 1841 1845 1846 1847 CONECT 1845 1844 CONECT 1846 1844 CONECT 1847 1844 MASTER 221 0 2 2 10 0 0 6 1031 2 38 10 END