HEADER PROTEIN BINDING 05-OCT-21 7PVT TITLE CRYSTAL STRUCTURE OF THE V-SRC SH3 DOMAIN Q128R MUTANT IN COMPLEX WITH TITLE 2 THE SYNTHETIC PEPTIDE VSL12 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN KINASE TRANSFORMING PROTEIN SRC; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: PP60V-SRC,P60-SRC,V-SRC; COMPND 5 EC: 2.7.10.2; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: VSL12; COMPND 10 CHAIN: B, D; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ROUS SARCOMA VIRUS (STRAIN SCHMIDT-RUPPIN E); SOURCE 3 ORGANISM_COMMON: RSV-SR-E; SOURCE 4 ORGANISM_TAXID: 270623; SOURCE 5 STRAIN: SCHMIDT-RUPPIN E; SOURCE 6 GENE: V-SRC; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PHTP1; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: UNIDENTIFIED; SOURCE 14 ORGANISM_TAXID: 32644 KEYWDS BETA BARREL, SH3 DOMAIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR A.CAMARA-ARTIGAS,M.C.SALINAS-GARCIA REVDAT 2 31-JAN-24 7PVT 1 REMARK REVDAT 1 14-SEP-22 7PVT 0 JRNL AUTH A.CAMARA-ARTIGAS,M.C.SALINAS GARCIA JRNL TITL CRYSTAL STRUCTURE OF THE V-SRC SH3 DOMAIN Q128R MUTANT IN JRNL TITL 2 COMPLEX WITH THE SYNTHETIC PEPTIDE VSL12 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.140 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 35656 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1785 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 17.1800 - 3.7500 1.00 2623 141 0.1511 0.1786 REMARK 3 2 3.7500 - 2.9800 1.00 2586 156 0.1657 0.2004 REMARK 3 3 2.9800 - 2.6100 0.98 2571 140 0.1956 0.2476 REMARK 3 4 2.6100 - 2.3700 0.97 2522 176 0.2025 0.1859 REMARK 3 5 2.3700 - 2.2000 1.00 2647 92 0.1967 0.1731 REMARK 3 6 2.2000 - 2.0700 1.00 2639 128 0.1769 0.2240 REMARK 3 7 2.0700 - 1.9700 1.00 2587 132 0.1442 0.1775 REMARK 3 8 1.9600 - 1.8800 1.00 2672 132 0.1579 0.2393 REMARK 3 9 1.8800 - 1.8100 1.00 2585 132 0.2092 0.2219 REMARK 3 10 1.8100 - 1.7500 1.00 2610 176 0.2245 0.2295 REMARK 3 11 1.7500 - 1.6900 1.00 2619 136 0.2468 0.2608 REMARK 3 12 1.6900 - 1.6400 1.00 2569 88 0.2886 0.2810 REMARK 3 13 1.6400 - 1.6000 1.00 2641 156 0.3034 0.3500 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) : 28.030 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.70 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 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7PVT 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_1292118487. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96770 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.7 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17900 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 17.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.80200 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: 7NER REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4 M AMMONIUM SULFATE, 10% GLICEROL, REMARK 280 5% PEG300, 40 MM LICL, 0.1M MES, PH 6.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 283K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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 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 30.89333 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 15.44667 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: DIMERIC 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 ASN A 112 REMARK 465 ASN A 113 REMARK 465 THR A 114 REMARK 465 GLU A 115 REMARK 465 ASP A 141 REMARK 465 VAL B 1 REMARK 465 SER B 2 REMARK 465 GLY C 81 REMARK 465 GLY C 82 REMARK 465 VAL C 83 REMARK 465 SER C 140 REMARK 465 ASP C 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 LYS A 103 CG CD CE NZ REMARK 470 ARG B 5 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 97 CG CD OE1 OE2 REMARK 470 LYS C 103 CG CD CE NZ REMARK 470 ARG C 107 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 115 CG CD OE1 OE2 REMARK 470 VAL D 1 CG1 CG2 REMARK 470 ARG D 5 CG CD NE CZ NH1 NH2 DBREF 7PVT A 81 141 UNP P63185 SRC_RSVSE 81 141 DBREF 7PVT B 1 12 PDB 7PVT 7PVT 1 12 DBREF 7PVT C 81 141 UNP P63185 SRC_RSVSE 81 141 DBREF 7PVT D 1 12 PDB 7PVT 7PVT 1 12 SEQADV 7PVT ARG A 128 UNP P63185 GLN 128 ENGINEERED MUTATION SEQADV 7PVT ARG C 128 UNP P63185 GLN 128 ENGINEERED MUTATION SEQRES 1 A 61 GLY GLY VAL THR THR PHE VAL ALA LEU TYR ASP TYR GLU SEQRES 2 A 61 SER TRP ILE 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 ARG THR GLY TYR ILE SEQRES 5 A 61 PRO SER ASN TYR VAL ALA PRO SER ASP SEQRES 1 B 12 VAL SER LEU ALA ARG ARG PRO LEU PRO PRO LEU PRO SEQRES 1 C 61 GLY GLY VAL THR THR PHE VAL ALA LEU TYR ASP TYR GLU SEQRES 2 C 61 SER TRP ILE GLU THR ASP LEU SER PHE LYS LYS GLY GLU SEQRES 3 C 61 ARG LEU GLN ILE VAL ASN ASN THR GLU GLY ASN TRP TRP SEQRES 4 C 61 LEU ALA HIS SER VAL THR THR GLY ARG THR GLY TYR ILE SEQRES 5 C 61 PRO SER ASN TYR VAL ALA PRO SER ASP SEQRES 1 D 12 VAL SER LEU ALA ARG ARG PRO LEU PRO PRO LEU PRO HET PEG A 201 17 HET GOL C 201 14 HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 PEG C4 H10 O3 FORMUL 6 GOL C3 H8 O3 FORMUL 7 HOH *56(H2 O) SHEET 1 AA1 5 THR A 129 PRO A 133 0 SHEET 2 AA1 5 TRP A 118 HIS A 122 -1 N ALA A 121 O GLY A 130 SHEET 3 AA1 5 ARG A 107 ILE A 110 -1 N GLN A 109 O HIS A 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 A 137 PRO A 139 -1 O ALA A 138 N VAL A 87 SHEET 1 AA2 5 THR C 129 PRO C 133 0 SHEET 2 AA2 5 TRP C 118 HIS C 122 -1 N ALA C 121 O GLY C 130 SHEET 3 AA2 5 ARG C 107 ASN C 112 -1 N VAL C 111 O LEU C 120 SHEET 4 AA2 5 THR C 85 ALA C 88 -1 N PHE C 86 O LEU C 108 SHEET 5 AA2 5 VAL C 137 ALA C 138 -1 O ALA C 138 N VAL C 87 CRYST1 51.227 51.227 46.340 90.00 90.00 120.00 P 32 6 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 0.019521 0.011270 0.000000 0.00000 SCALE2 0.000000 0.022541 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021579 0.00000