HEADER SIGNALING PROTEIN/PEPTIDE 07-NOV-12 4HVV TITLE CRYSTAL STRUCTURE OF THE T98E C-SRC-SH3 DOMAIN 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: SYNTHETIC PEPTIDE ACETYL-APPLPPRNRP; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: BANTAM,CHICKENS; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 GENE: SRC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: HIGH AFFINITY PEPTIDE DESIGNED FROM PHAGE DISPLAY SOURCE 14 EXPERIMENTS KEYWDS BETA SHANDWICH, SH3 LIKE BARREL, KINASE, PROLINE RICH MOTIFS, KEYWDS 2 SIGNALING PROTEIN-PEPTIDE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.CAMARA-ARTIGAS REVDAT 3 20-SEP-23 4HVV 1 REMARK SEQADV LINK REVDAT 2 19-JUN-13 4HVV 1 JRNL REVDAT 1 01-MAY-13 4HVV 0 JRNL AUTH J.BACARIZO,A.CAMARA-ARTIGAS JRNL TITL ATOMIC RESOLUTION STRUCTURES OF THE C-SRC SH3 DOMAIN IN JRNL TITL 2 COMPLEX WITH TWO HIGH-AFFINITY PEPTIDES FROM CLASSES I AND JRNL TITL 3 II. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 69 756 2013 JRNL REFN ISSN 0907-4449 JRNL PMID 23633584 JRNL DOI 10.1107/S0907444913001522 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 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) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.150 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 46049 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.144 REMARK 3 R VALUE (WORKING SET) : 0.144 REMARK 3 FREE R VALUE : 0.156 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 2365 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 19.1003 - 2.8258 0.93 2521 126 0.1767 0.1800 REMARK 3 2 2.8258 - 2.2441 1.00 2714 126 0.1608 0.1412 REMARK 3 3 2.2441 - 1.9607 1.00 2685 138 0.1242 0.1564 REMARK 3 4 1.9607 - 1.7816 1.00 2692 143 0.1167 0.1250 REMARK 3 5 1.7816 - 1.6540 1.00 2694 167 0.1100 0.1407 REMARK 3 6 1.6540 - 1.5565 1.00 2746 116 0.1069 0.1304 REMARK 3 7 1.5565 - 1.4786 1.00 2677 170 0.1064 0.1412 REMARK 3 8 1.4786 - 1.4142 1.00 2685 165 0.1131 0.1270 REMARK 3 9 1.4142 - 1.3598 1.00 2669 161 0.1102 0.1062 REMARK 3 10 1.3598 - 1.3129 1.00 2672 149 0.1106 0.1537 REMARK 3 11 1.3129 - 1.2719 1.00 2702 149 0.1293 0.1857 REMARK 3 12 1.2719 - 1.2355 1.00 2720 164 0.1436 0.1781 REMARK 3 13 1.2355 - 1.2030 1.00 2684 167 0.1443 0.1914 REMARK 3 14 1.2030 - 1.1736 0.95 2520 122 0.1529 0.1774 REMARK 3 15 1.1736 - 1.1470 0.86 2347 110 0.1745 0.2010 REMARK 3 16 1.1470 - 1.1226 0.77 2098 111 0.1995 0.2439 REMARK 3 17 1.1226 - 1.1001 0.68 1858 81 0.2496 0.2793 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.52 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.73 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 : 0.009 571 REMARK 3 ANGLE : 1.214 781 REMARK 3 CHIRALITY : 0.073 82 REMARK 3 PLANARITY : 0.007 101 REMARK 3 DIHEDRAL : 12.400 211 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 4HVV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000075984. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-APR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 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) : 0.97 REMARK 200 MONOCHROMATOR : SI(111) CHANNEL-CUT CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.1.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24885 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 35.563 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.66700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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: PDB ENTRY 3FJ5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.7 M AMMONIUM SULPHATE, 10% PEG 300, REMARK 280 10% GLYCEROL AND 0.1 M SODIUM ACETATE, PH 5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-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 35.56300 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 71.12600 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 71.12600 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 35.56300 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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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: 1220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 SER A 82 REMARK 465 HIS A 83 REMARK 465 MET A 84 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 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4HVU RELATED DB: PDB REMARK 900 RELATED ID: 4HVW RELATED DB: PDB REMARK 900 RELATED ID: 1QWE RELATED DB: PDB REMARK 900 C-SRC SH3 DOMAIN COMPLEXED WITH LIGAND APP12 (NMR STRUCTURE) REMARK 900 RELATED ID: 1QWF RELATED DB: PDB REMARK 900 C-SRC SH3 DOMAIN COMPLEXED WITH LIGAND VSL12 (NMR STRUCTURE) REMARK 900 RELATED ID: 3FJ5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE C-SRC-SH3 DOMAIN REMARK 900 RELATED ID: 1SRL RELATED DB: PDB REMARK 900 1H AND 15N ASSIGNMENTS AND SECONDARY STRUCTURE OF THE SRC SH3 DOMAIN DBREF 4HVV A 85 140 UNP P00523 SRC_CHICK 85 140 DBREF 4HVV B 0 10 PDB 4HVV 4HVV 0 10 SEQADV 4HVV GLY A 81 UNP P00523 EXPRESSION TAG SEQADV 4HVV SER A 82 UNP P00523 EXPRESSION TAG SEQADV 4HVV HIS A 83 UNP P00523 EXPRESSION TAG SEQADV 4HVV MET A 84 UNP P00523 EXPRESSION TAG SEQADV 4HVV GLU A 98 UNP P00523 THR 98 ENGINEERED MUTATION SEQADV 4HVV ARG A 128 UNP P00523 GLN 128 ENGINEERED MUTATION SEQRES 1 A 60 GLY SER HIS MET THR PHE VAL ALA LEU TYR ASP TYR GLU SEQRES 2 A 60 SER ARG THR GLU GLU ASP LEU SER PHE LYS LYS GLY GLU SEQRES 3 A 60 ARG LEU GLN ILE VAL ASN ASN THR GLU GLY ASP TRP TRP SEQRES 4 A 60 LEU ALA HIS SER LEU THR THR GLY ARG THR GLY TYR ILE SEQRES 5 A 60 PRO SER ASN TYR VAL ALA PRO SER SEQRES 1 B 11 ACE ALA PRO PRO LEU PRO PRO ARG ASN ARG PRO 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 *73(H2 O) SHEET 1 A 5 THR A 129 PRO A 133 0 SHEET 2 A 5 TRP A 118 SER A 123 -1 N ALA A 121 O GLY A 130 SHEET 3 A 5 ARG A 107 ASN A 112 -1 N GLN A 109 O HIS A 122 SHEET 4 A 5 PHE A 86 ALA A 88 -1 N PHE A 86 O LEU A 108 SHEET 5 A 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 1.33 SITE 1 AC1 6 GLU A 93 SER A 94 SER A 101 HOH A 302 SITE 2 AC1 6 HOH A 307 ARG B 9 CRYST1 31.588 31.588 106.689 90.00 90.00 120.00 P 31 2 1 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 0.031657 0.018277 0.000000 0.00000 SCALE2 0.000000 0.036554 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009373 0.00000