HEADER PROTEIN BINDING 18-AUG-20 7A33 TITLE CRYSTAL STRUCTURE OF THE C-SRC SH3 DOMAIN MUTANT S94A-T98D-V111L- TITLE 2 N113S-T114S AT PH 3.0 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 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.PLAZA-GARRIDO,M.C.SALINAS-GARCIA REVDAT 2 31-JAN-24 7A33 1 REMARK REVDAT 1 25-AUG-21 7A33 0 JRNL AUTH A.CAMARA-ARTIGAS,M.PLAZA-GARRIDO,M.C.SALINAS-GARCIA JRNL TITL CRYSTAL STRUCTURE OF THE C-SRC SH3 DOMAIN MUTANT JRNL TITL 2 S94A-T98D-V111L-N113S-T114S AT PH 3.0 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 0.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2 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) : 0.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.8 REMARK 3 NUMBER OF REFLECTIONS : 91360 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.119 REMARK 3 R VALUE (WORKING SET) : 0.119 REMARK 3 FREE R VALUE : 0.134 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 4514 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 19.2200 - 2.9700 0.90 3023 146 0.1148 0.1262 REMARK 3 2 2.9700 - 2.3600 0.90 2984 152 0.1366 0.1521 REMARK 3 3 2.3600 - 2.0600 0.91 3060 132 0.1157 0.1232 REMARK 3 4 2.0600 - 1.8700 0.88 2903 155 0.1057 0.1178 REMARK 3 5 1.8700 - 1.7400 0.88 2977 141 0.1143 0.1222 REMARK 3 6 1.7400 - 1.6300 0.90 3012 158 0.1067 0.1275 REMARK 3 7 1.6300 - 1.5500 0.92 3047 175 0.1044 0.1392 REMARK 3 8 1.5500 - 1.4900 0.91 3077 145 0.1026 0.1057 REMARK 3 9 1.4900 - 1.4300 0.88 2876 157 0.1002 0.1196 REMARK 3 10 1.4300 - 1.3800 0.92 3066 161 0.1056 0.1107 REMARK 3 11 1.3800 - 1.3400 0.90 3059 149 0.1030 0.1363 REMARK 3 12 1.3400 - 1.3000 0.93 3043 174 0.1051 0.1241 REMARK 3 13 1.3000 - 1.2600 0.90 3063 161 0.1053 0.1419 REMARK 3 14 1.2600 - 1.2300 0.92 3009 186 0.1083 0.1194 REMARK 3 15 1.2300 - 1.2000 0.88 2897 144 0.1054 0.1346 REMARK 3 16 1.2000 - 1.1800 0.88 2998 152 0.1035 0.1162 REMARK 3 17 1.1800 - 1.1600 0.91 2992 154 0.1036 0.1139 REMARK 3 18 1.1600 - 1.1300 0.87 2924 149 0.1032 0.1162 REMARK 3 19 1.1300 - 1.1100 0.90 2960 174 0.1108 0.1317 REMARK 3 20 1.1100 - 1.0900 0.89 3018 128 0.1108 0.1354 REMARK 3 21 1.0900 - 1.0800 0.87 2867 182 0.1163 0.1337 REMARK 3 22 1.0800 - 1.0600 0.86 2903 122 0.1230 0.1260 REMARK 3 23 1.0600 - 1.0400 0.87 2914 136 0.1306 0.1423 REMARK 3 24 1.0400 - 1.0300 0.87 2920 144 0.1461 0.1853 REMARK 3 25 1.0300 - 1.0200 0.87 2891 173 0.1645 0.1907 REMARK 3 26 1.0200 - 1.0000 0.86 2833 144 0.1826 0.2100 REMARK 3 27 1.0000 - 0.9900 0.81 2754 141 0.2044 0.2119 REMARK 3 28 0.9900 - 0.9800 0.75 2466 136 0.2412 0.2233 REMARK 3 29 0.9800 - 0.9700 0.69 2253 135 0.2796 0.3227 REMARK 3 30 0.9700 - 0.9600 0.60 2057 108 0.3117 0.3167 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.65 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 7A33 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_1292110780. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.0 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) : 0.9790 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 0.6.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 91360 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.960 REMARK 200 RESOLUTION RANGE LOW (A) : 19.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.41600 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: 4JZ4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 24.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5 MM BETA-CYCLODEXTRIN, 1.5 M AMMOMIUM REMARK 280 SULFATE, 0.1M SODIUM CITRATE, PH 3.0, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 31.63100 REMARK 290 SMTRY3 2 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 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 REMARK 465 SER B 140 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 115 CG CD OE1 OE2 REMARK 470 SER A 140 OG 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 GLU B 115 58.63 -96.69 REMARK 500 REMARK 500 REMARK: NULL 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 370 DISTANCE = 6.41 ANGSTROMS REMARK 525 HOH B 380 DISTANCE = 6.71 ANGSTROMS 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 B 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 113 O REMARK 620 2 GLY B 116 O 94.7 REMARK 620 3 HOH B 355 O 96.5 113.1 REMARK 620 4 HOH B 362 O 178.7 84.6 82.7 REMARK 620 5 HOH B 364 O 92.5 109.3 135.7 88.8 REMARK 620 N 1 2 3 4 DBREF 7A33 A 82 141 UNP P00523 SRC_CHICK 82 141 DBREF 7A33 B 82 141 UNP P00523 SRC_CHICK 82 141 SEQADV 7A33 ALA A 94 UNP P00523 SER 94 ENGINEERED MUTATION SEQADV 7A33 ASP A 98 UNP P00523 THR 98 ENGINEERED MUTATION SEQADV 7A33 LEU A 111 UNP P00523 VAL 111 ENGINEERED MUTATION SEQADV 7A33 SER A 113 UNP P00523 ASN 113 ENGINEERED MUTATION SEQADV 7A33 SER A 114 UNP P00523 THR 114 ENGINEERED MUTATION SEQADV 7A33 ALA B 94 UNP P00523 SER 94 ENGINEERED MUTATION SEQADV 7A33 ASP B 98 UNP P00523 THR 98 ENGINEERED MUTATION SEQADV 7A33 LEU B 111 UNP P00523 VAL 111 ENGINEERED MUTATION SEQADV 7A33 SER B 113 UNP P00523 ASN 113 ENGINEERED MUTATION SEQADV 7A33 SER B 114 UNP P00523 THR 114 ENGINEERED MUTATION SEQRES 1 A 60 GLY VAL THR THR PHE VAL ALA LEU TYR ASP TYR GLU ALA SEQRES 2 A 60 ARG THR GLU ASP ASP LEU SER PHE LYS LYS GLY GLU ARG SEQRES 3 A 60 LEU GLN ILE LEU ASN SER SER GLU 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 GLU ALA SEQRES 2 B 60 ARG THR GLU ASP ASP LEU SER PHE LYS LYS GLY GLU ARG SEQRES 3 B 60 LEU GLN ILE LEU ASN SER SER GLU 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 FMT A 201 5 HET FMT A 202 5 HET FMT B 201 5 HET NA B 202 1 HETNAM FMT FORMIC ACID HETNAM NA SODIUM ION FORMUL 3 FMT 3(C H2 O2) FORMUL 6 NA NA 1+ FORMUL 7 HOH *150(H2 O) SHEET 1 AA1 5 THR A 129 PRO A 133 0 SHEET 2 AA1 5 TRP A 118 SER A 123 -1 N ALA A 121 O GLY A 130 SHEET 3 AA1 5 ARG A 107 ASN A 112 -1 N LEU A 111 O LEU A 120 SHEET 4 AA1 5 PHE A 86 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 B 129 PRO B 133 0 SHEET 2 AA2 5 TRP B 118 SER B 123 -1 N ALA B 121 O GLY B 130 SHEET 3 AA2 5 ARG B 107 GLU B 115 -1 N ASN B 112 O LEU B 120 SHEET 4 AA2 5 PHE B 86 ALA B 88 -1 N PHE B 86 O LEU B 108 SHEET 5 AA2 5 VAL B 137 ALA B 138 -1 O ALA B 138 N VAL B 87 LINK O SER B 113 NA NA B 202 1555 1555 2.29 LINK O GLY B 116 NA NA B 202 1555 1555 2.37 LINK NA NA B 202 O HOH B 355 1555 1555 2.38 LINK NA NA B 202 O HOH B 362 1555 1555 2.38 LINK NA NA B 202 O HOH B 364 1555 1555 2.29 CRYST1 23.203 63.262 30.073 90.00 95.65 90.00 P 1 21 1 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 0.043098 0.000000 0.004265 0.00000 SCALE2 0.000000 0.015807 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033415 0.00000