HEADER TRANSFERASE 25-JUN-17 5OB0 TITLE CRYSTAL STRUCTURE OF THE C-SRC-SH3 DOMAIN Q128E MUTANT IN COMPLEX WITH TITLE 2 THE HIGH AFFINITY PEPTIDE APP12 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; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: APP12; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: 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; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS BETA SHANDWICH, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.CAMARA-ARTIGAS REVDAT 5 17-JAN-24 5OB0 1 REMARK REVDAT 4 20-FEB-19 5OB0 1 SOURCE REVDAT 3 24-JAN-18 5OB0 1 SOURCE REVDAT 2 13-SEP-17 5OB0 1 REMARK REVDAT 1 12-JUL-17 5OB0 0 JRNL AUTH A.CAMARA-ARTIGAS JRNL TITL CRYSTAL STRUCTURE OF THE C-SRC-SH3 DOMAIN Q128E MUTANT IN JRNL TITL 2 COMPLEX WITH THE HIGH AFFINITY PEPTIDE APP12 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.17 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.780 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 41471 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.132 REMARK 3 R VALUE (WORKING SET) : 0.131 REMARK 3 FREE R VALUE : 0.149 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 2051 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 25.5699 - 2.8891 0.86 2319 141 0.1585 0.1719 REMARK 3 2 2.8891 - 2.2937 0.98 2623 134 0.1391 0.1392 REMARK 3 3 2.2937 - 2.0039 0.97 2617 141 0.1100 0.0965 REMARK 3 4 2.0039 - 1.8207 0.98 2612 143 0.1179 0.1326 REMARK 3 5 1.8207 - 1.6902 0.98 2693 107 0.1197 0.1568 REMARK 3 6 1.6902 - 1.5906 0.99 2666 133 0.1115 0.1465 REMARK 3 7 1.5906 - 1.5109 0.99 2644 139 0.1145 0.1499 REMARK 3 8 1.5109 - 1.4452 0.99 2706 140 0.1219 0.1584 REMARK 3 9 1.4452 - 1.3895 0.99 2655 143 0.1252 0.1402 REMARK 3 10 1.3895 - 1.3416 0.99 2647 146 0.1295 0.1623 REMARK 3 11 1.3416 - 1.2997 0.99 2679 131 0.1319 0.1917 REMARK 3 12 1.2997 - 1.2625 0.98 2621 153 0.1342 0.1727 REMARK 3 13 1.2625 - 1.2293 0.99 2685 127 0.1336 0.1410 REMARK 3 14 1.2293 - 1.1993 0.99 2667 146 0.1479 0.1944 REMARK 3 15 1.1993 - 1.1720 0.95 2586 127 0.1692 0.2100 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.36 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.18 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 : 0.009 599 REMARK 3 ANGLE : 1.164 824 REMARK 3 CHIRALITY : 0.081 87 REMARK 3 PLANARITY : 0.010 110 REMARK 3 DIHEDRAL : 16.310 222 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 5OB0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1200005498. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-13 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 : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9334 REMARK 200 MONOCHROMATOR : SI(111) CHANNEL-CUT CRYSTAL REMARK 200 MONOCHROMATOR AND A PAIR OF KB REMARK 200 MIRRORS REMARK 200 OPTICS : VERTICAL FOCUSING MIRROR (VFM) REMARK 200 AND A HORIZONTAL FOCUSING REMARK 200 MIRROR(HFM), MANUFACTURED BY REMARK 200 IRELEC. REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.3.11 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41471 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.170 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.16600 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: 4ZJ4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.9 M AMMONIUM SULPHATE, 0.05 M SODIUM REMARK 280 CHLORIDE, 0.1 M SODIUM ACETATE AND 10% GLYCEROL, PH 4.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-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 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 8.46352 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.28000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 31.79211 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 8.46352 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 16.28000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 31.79211 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: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 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 OE1 GLU A 93 LIES ON A SPECIAL POSITION. 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 SER A 82 REMARK 465 HIS A 83 REMARK 465 MET A 84 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 SER A 140 -162.95 -117.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 201 DBREF 5OB0 A 85 141 UNP P00523 SRC_CHICK 85 141 DBREF 5OB0 B 0 12 PDB 5OB0 5OB0 0 12 SEQADV 5OB0 GLY A 81 UNP P00523 EXPRESSION TAG SEQADV 5OB0 SER A 82 UNP P00523 EXPRESSION TAG SEQADV 5OB0 HIS A 83 UNP P00523 EXPRESSION TAG SEQADV 5OB0 MET A 84 UNP P00523 EXPRESSION TAG SEQADV 5OB0 GLU A 128 UNP P00523 GLN 128 ENGINEERED MUTATION SEQRES 1 A 61 GLY SER HIS MET 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 ASP TRP TRP SEQRES 4 A 61 LEU ALA HIS SER LEU THR THR GLY GLU THR GLY TYR ILE SEQRES 5 A 61 PRO SER ASN TYR VAL ALA PRO SER ASP SEQRES 1 B 13 ACE ALA PRO PRO LEU PRO PRO ARG ASN ARG PRO ARG LEU HET ACE B 0 3 HET SO4 A 201 5 HETNAM ACE ACETYL GROUP HETNAM SO4 SULFATE ION FORMUL 2 ACE C2 H4 O FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *94(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 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 LINK C ACE B 0 N ALA B 1 1555 1555 1.34 SITE 1 AC1 7 SER A 94 SER A 101 HOH A 305 HOH A 316 SITE 2 AC1 7 HOH A 320 HOH A 333 HOH A 350 CRYST1 31.630 32.560 65.262 90.00 103.02 90.00 I 1 2 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 0.031616 0.000000 0.007309 0.00000 SCALE2 0.000000 0.030713 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015727 0.00000