HEADER TRANSFERASE 20-OCT-15 5ECA TITLE CRYSTAL STRUCTURE OF A CHIMERIC C-SRC-SH3 DOMAIN WITH THE SEQUENCE OF TITLE 2 THE RT-LOOP FROM THE ABL-SH3 DOMAIN AT PH 6.5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SH3 DOMAIN; COMPND 5 SYNONYM: PROTO-ONCOGENE C-SRC,PP60C-SRC,P60-SRC; COMPND 6 EC: 2.7.10.2; COMPND 7 ENGINEERED: YES; COMPND 8 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: PET15B KEYWDS BETA SHANDWICH, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.CAMARA-ARTIGAS REVDAT 2 13-SEP-17 5ECA 1 REMARK REVDAT 1 09-NOV-16 5ECA 0 JRNL AUTH A.CAMARA-ARTIGAS JRNL TITL CRYSTAL STRUCTURE OF A CHIMERIC C-SRC-SH3 DOMAIN WITH THE JRNL TITL 2 SEQUENCE OF THE RT-LOOP FROM THE ABL-SH3 DOMAIN AT PH 6.5 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.160 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 39402 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 1924 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 19.0779 - 2.7932 0.99 2731 117 0.1678 0.1832 REMARK 3 2 2.7932 - 2.2182 0.99 2692 127 0.1574 0.1690 REMARK 3 3 2.2182 - 1.9381 0.98 2625 163 0.1292 0.1499 REMARK 3 4 1.9381 - 1.7610 0.98 2689 146 0.1316 0.1894 REMARK 3 5 1.7610 - 1.6349 0.99 2659 152 0.1441 0.1762 REMARK 3 6 1.6349 - 1.5385 0.99 2713 129 0.1360 0.1675 REMARK 3 7 1.5385 - 1.4615 0.99 2679 144 0.1440 0.1894 REMARK 3 8 1.4615 - 1.3979 0.99 2672 154 0.1545 0.1692 REMARK 3 9 1.3979 - 1.3441 0.99 2729 139 0.1665 0.1811 REMARK 3 10 1.3441 - 1.2977 0.99 2667 119 0.1740 0.2255 REMARK 3 11 1.2977 - 1.2572 0.98 2663 141 0.1902 0.2313 REMARK 3 12 1.2572 - 1.2212 0.98 2671 141 0.2134 0.2058 REMARK 3 13 1.2212 - 1.1891 0.98 2676 105 0.2303 0.2801 REMARK 3 14 1.1891 - 1.1601 0.97 2612 147 0.2346 0.2833 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.040 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.89 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 : 0.007 484 REMARK 3 ANGLE : 0.930 661 REMARK 3 CHIRALITY : 0.075 72 REMARK 3 PLANARITY : 0.005 84 REMARK 3 DIHEDRAL : 15.176 164 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 5ECA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214702. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-FEB-15 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 : ESRF REMARK 200 BEAMLINE : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.965 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.12 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20716 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.160 REMARK 200 RESOLUTION RANGE LOW (A) : 19.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.53700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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 (%): 44.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 M AMMONIUM SULPHATE, 0.1 M MES, PH REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 26.05650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.05650 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 20.42500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.00150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 20.42500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.00150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 26.05650 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 20.42500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 28.00150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 26.05650 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 20.42500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 28.00150 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 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 202 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 215 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 257 LIES ON A SPECIAL POSITION. 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 97 CG CD OE1 OE2 DBREF 5ECA A 85 141 UNP P00523 SRC_CHICK 85 141 SEQADV 5ECA SER A 82 UNP P00523 EXPRESSION TAG SEQADV 5ECA HIS A 83 UNP P00523 EXPRESSION TAG SEQADV 5ECA MET A 84 UNP P00523 EXPRESSION TAG SEQADV 5ECA VAL A 93 UNP P00523 GLU 93 ENGINEERED MUTATION SEQADV 5ECA ALA A 94 UNP P00523 SER 94 ENGINEERED MUTATION SEQADV 5ECA SER A 95 UNP P00523 ARG 95 ENGINEERED MUTATION SEQADV 5ECA GLY A 96 UNP P00523 THR 96 CONFLICT SEQADV 5ECA ARG A 128 UNP P00523 GLN 128 ENGINEERED MUTATION SEQRES 1 A 60 SER HIS MET 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 ASN ASN THR GLU GLY ASP TRP TRP LEU SEQRES 4 A 60 ALA HIS SER LEU THR THR GLY ARG THR GLY TYR ILE PRO SEQRES 5 A 60 SER ASN TYR VAL ALA PRO SER ASP FORMUL 2 HOH *68(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 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 CRYST1 40.850 56.003 52.113 90.00 90.00 90.00 C 2 2 21 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 0.024480 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017856 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019189 0.00000 MASTER 237 0 0 0 5 0 0 6 0 0 0 5 END