HEADER PROTEIN BINDING 04-FEB-21 7NET TITLE CRYSTAL STRUCTURE OF THE V-SRC SH3 DOMAIN W95R-I96T MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: V-SRC SH3 DOMAIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 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 31-JAN-24 7NET 1 REMARK REVDAT 2 16-JUN-21 7NET 1 JRNL REVDAT 1 02-JUN-21 7NET 0 JRNL AUTH M.C.SALINAS-GARCIA,M.PLAZA-GARRIDO,A.CAMARA-ARTIGAS JRNL TITL THE IMPACT OF ONCOGENIC MUTATIONS OF THE VIRAL SRC KINASE ON JRNL TITL 2 THE STRUCTURE AND STABILITY OF THE SH3 DOMAIN. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 77 854 2021 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 34076598 JRNL DOI 10.1107/S2059798321004344 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.C.SALINAS-GARCIA,M.PLAZA-GARRIDO,A.CAMARA-ARTIGAS REMARK 1 TITL THE IMPACT OF ONCOGENIC MUTATIONS OF THE VIRAL SRC KINASE ON REMARK 1 TITL 2 THE STRUCTURE AND STABILITY OF THE SH3 DOMAIN REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D 2021 REMARK 1 REFN ESSN 1399-0047 REMARK 1 DOI HTTPS://DOI.ORG/10.1107/S2059798321004344 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1-4122 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) : 19.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.290 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 24656 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2333 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 19.9500 - 3.8500 0.97 2665 175 0.1760 0.1631 REMARK 3 2 3.8500 - 3.0600 0.97 2725 137 0.1654 0.2123 REMARK 3 3 3.0600 - 2.6700 0.97 2694 146 0.2111 0.2185 REMARK 3 4 2.6700 - 2.4300 0.97 2636 198 0.2072 0.2116 REMARK 3 5 2.4300 - 2.2500 0.98 2707 176 0.1913 0.2168 REMARK 3 6 2.2500 - 2.1200 0.95 2613 137 0.1937 0.1767 REMARK 3 7 2.1200 - 2.0200 0.96 2740 94 0.1897 0.1341 REMARK 3 8 2.0200 - 1.9300 0.97 2690 156 0.1497 0.2026 REMARK 3 9 1.9300 - 1.8500 0.97 2739 110 0.1658 0.1490 REMARK 3 10 1.8500 - 1.7900 0.96 2657 143 0.2006 0.2200 REMARK 3 11 1.7900 - 1.7300 0.95 2686 127 0.1747 0.1972 REMARK 3 12 1.7300 - 1.6800 0.96 2681 129 0.1793 0.2061 REMARK 3 13 1.6800 - 1.6400 0.97 2732 132 0.2066 0.2165 REMARK 3 14 1.6400 - 1.6000 0.96 2639 160 0.2064 0.2756 REMARK 3 15 1.6000 - 1.5600 0.92 2581 114 0.2201 0.2396 REMARK 3 16 1.5600 - 1.5300 0.81 2278 95 0.2296 0.2763 REMARK 3 17 1.5300 - 1.5000 0.72 1987 104 0.2474 0.2951 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.660 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.70 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 : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN A AND (RESID 84 THROUGH 93 OR REMARK 3 RESID 96 THROUGH 98 OR RESID 100 THROUGH REMARK 3 112 OR RESID 114 THROUGH 140)) REMARK 3 SELECTION : (CHAIN C AND (RESID 84 THROUGH 93 OR REMARK 3 RESID 96 THROUGH 98 OR RESID 100 THROUGH REMARK 3 109 OR (RESID 110 AND (NAME N OR NAME CA REMARK 3 OR NAME C OR NAME O OR NAME CB )) OR REMARK 3 RESID 111 THROUGH 112 OR RESID 114 REMARK 3 THROUGH 140)) REMARK 3 ATOM PAIRS NUMBER : 462 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7NET COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1292113770. 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 : 6.5 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 : 24714 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 19.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.02600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.3000 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 (%) : 83.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.42500 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: 6XVO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M AMMONIUM SULFATE, 5% PEG 300, 10% REMARK 280 GLYCEROL, 40 MM LICL AND 0.1M MES, PH 6.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 85.31133 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 42.65567 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 63.98350 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 21.32783 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 106.63917 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: 5980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 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 GLY A 81 REMARK 465 GLY A 82 REMARK 465 VAL A 83 REMARK 465 ASP A 141 REMARK 465 GLY B 81 REMARK 465 GLY B 82 REMARK 465 VAL B 83 REMARK 465 ASP B 141 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 93 CG CD OE1 OE2 REMARK 470 ILE A 110 CG1 CG2 CD1 REMARK 470 GLU B 93 CG CD OE1 OE2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 203 DBREF 7NET A 81 141 PDB 7NET 7NET 81 141 DBREF 7NET B 81 141 PDB 7NET 7NET 81 141 SEQRES 1 A 61 GLY GLY VAL THR THR PHE VAL ALA LEU TYR ASP TYR GLU SEQRES 2 A 61 SER ARG THR GLU THR ASP LEU SER PHE LYS LYS GLY GLU SEQRES 3 A 61 ARG LEU GLN ILE VAL ASN ASN THR GLU GLY ASN TRP TRP SEQRES 4 A 61 LEU ALA HIS SER VAL THR THR GLY GLN THR GLY TYR ILE SEQRES 5 A 61 PRO SER ASN TYR VAL ALA PRO SER ASP SEQRES 1 B 61 GLY GLY VAL THR THR PHE VAL ALA LEU TYR ASP TYR GLU SEQRES 2 B 61 SER ARG THR GLU THR ASP LEU SER PHE LYS LYS GLY GLU SEQRES 3 B 61 ARG LEU GLN ILE VAL ASN ASN THR GLU GLY ASN TRP TRP SEQRES 4 B 61 LEU ALA HIS SER VAL THR THR GLY GLN THR GLY TYR ILE SEQRES 5 B 61 PRO SER ASN TYR VAL ALA PRO SER ASP HET PEG A 201 17 HET PEG A 202 17 HET PGE A 203 24 HET PEG B 201 17 HET PEG B 202 17 HET SO4 B 203 5 HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM PGE TRIETHYLENE GLYCOL HETNAM SO4 SULFATE ION FORMUL 3 PEG 4(C4 H10 O3) FORMUL 5 PGE C6 H14 O4 FORMUL 8 SO4 O4 S 2- FORMUL 9 HOH *67(H2 O) SHEET 1 AA1 5 THR B 129 PRO B 133 0 SHEET 2 AA1 5 TRP B 118 SER B 123 -1 N TRP B 119 O ILE B 132 SHEET 3 AA1 5 ARG A 107 ILE A 110 -1 N GLN A 109 O HIS B 122 SHEET 4 AA1 5 THR A 85 ALA A 88 -1 N PHE A 86 O LEU A 108 SHEET 5 AA1 5 VAL B 137 PRO B 139 -1 O ALA B 138 N VAL A 87 SHEET 1 AA2 5 THR A 129 PRO A 133 0 SHEET 2 AA2 5 TRP A 118 SER A 123 -1 N TRP A 119 O ILE A 132 SHEET 3 AA2 5 ARG B 107 ILE B 110 -1 O GLN B 109 N HIS A 122 SHEET 4 AA2 5 THR B 85 ALA B 88 -1 N PHE B 86 O LEU B 108 SHEET 5 AA2 5 VAL A 137 PRO A 139 -1 N ALA A 138 O VAL B 87 SITE 1 AC1 2 TYR A 90 LYS B 104 SITE 1 AC2 2 LYS A 104 GLY A 105 SITE 1 AC3 11 TYR A 92 ARG A 95 THR A 98 ASP A 99 SITE 2 AC3 11 TRP A 118 HOH A 301 ARG B 95 THR B 98 SITE 3 AC3 11 ASP B 99 TRP B 118 TYR B 131 SITE 1 AC4 4 LYS A 104 ASN A 135 TYR A 136 TYR B 90 SITE 1 AC5 1 LYS B 104 SITE 1 AC6 9 THR A 96 GLU A 97 HOH A 313 THR B 96 SITE 2 AC6 9 GLU B 97 HOH B 301 HOH B 303 HOH B 311 SITE 3 AC6 9 HOH B 321 CRYST1 46.648 46.648 127.967 90.00 90.00 120.00 P 65 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 0.021437 0.012377 0.000000 0.00000 SCALE2 0.000000 0.024753 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007815 0.00000