HEADER BLOOD CLOTTING, SIGNALING PROTEIN 11-NOV-12 4HXJ TITLE CRYSTAL STRUCTURE OF SH3:RGT COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: HUMAN C-SRC SH3 DOMAIN, UNP RESIDUES 87-144; COMPND 5 SYNONYM: C-SRC, PROTO-ONCOGENE C-SRC, PP60C-SRC, P60-SRC; COMPND 6 EC: 2.7.10.2; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: C-TERMINAL 3-MER PEPTIDE FROM INTEGRIN BETA-3; COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SRC, SRC1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET32A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 OTHER_DETAILS: THE RGT PEPTIDE WAS SYNTHESIZED IN THE SOLID PHASE KEYWDS INTEGRIN BETA-3, C-SRC KINASE, SH3 DOMAIN, RGT, THROMBOSIS, CELL KEYWDS 2 SIGNALING, BLOOD CLOTTING, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.XIAO,G.MENG REVDAT 4 08-NOV-23 4HXJ 1 SEQADV REVDAT 3 19-MAR-14 4HXJ 1 JRNL REVDAT 2 05-DEC-12 4HXJ 1 JRNL REVDAT 1 28-NOV-12 4HXJ 0 JRNL AUTH R.XIAO,X.D.XI,Z.CHEN,S.J.CHEN,G.MENG JRNL TITL STRUCTURAL FRAMEWORK OF C-SRC ACTIVATION BY INTEGRIN BETA 3 JRNL REF BLOOD V. 121 700 2013 JRNL REFN ISSN 0006-4971 JRNL PMID 23169783 JRNL DOI 10.1182/BLOOD-2012-07-440644 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.120 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 6144 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 614 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 29.1658 - 4.1572 0.99 1245 130 0.1496 0.1779 REMARK 3 2 4.1572 - 3.3012 1.00 1247 133 0.1194 0.1488 REMARK 3 3 3.3012 - 2.8843 1.00 1245 131 0.1257 0.1787 REMARK 3 4 2.8843 - 2.6208 0.99 1243 130 0.1430 0.2164 REMARK 3 5 2.6208 - 2.4330 0.99 1227 152 0.1576 0.2119 REMARK 3 6 2.4330 - 2.2896 0.99 1237 124 0.1486 0.2203 REMARK 3 7 2.2896 - 2.1750 0.98 1247 119 0.1356 0.2154 REMARK 3 8 2.1750 - 2.0804 0.98 1213 154 0.1406 0.1937 REMARK 3 9 2.0804 - 2.0003 0.98 1217 135 0.1349 0.2085 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 : 0.40 REMARK 3 B_SOL : 42.43 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.480 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.32650 REMARK 3 B22 (A**2) : -5.83230 REMARK 3 B33 (A**2) : -2.06350 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -3.68400 REMARK 3 B23 (A**2) : 0.00000 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 : 0.007 968 REMARK 3 ANGLE : 1.025 1321 REMARK 3 CHIRALITY : 0.075 147 REMARK 3 PLANARITY : 0.003 167 REMARK 3 DIHEDRAL : 16.389 318 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 6.6441 -9.2139 25.3687 REMARK 3 T TENSOR REMARK 3 T11: 0.0120 T22: 0.0265 REMARK 3 T33: 0.0364 T12: 0.0089 REMARK 3 T13: -0.0009 T23: -0.0058 REMARK 3 L TENSOR REMARK 3 L11: 0.0531 L22: 0.3803 REMARK 3 L33: 0.2076 L12: 0.0434 REMARK 3 L13: -0.0760 L23: -0.0983 REMARK 3 S TENSOR REMARK 3 S11: 0.0162 S12: -0.0076 S13: -0.0325 REMARK 3 S21: 0.0110 S22: -0.0521 S23: 0.0651 REMARK 3 S31: -0.0093 S32: 0.0238 S33: 0.0237 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 14.0201 -25.1396 37.8538 REMARK 3 T TENSOR REMARK 3 T11: 0.0127 T22: 0.0317 REMARK 3 T33: 0.0172 T12: 0.0094 REMARK 3 T13: 0.0095 T23: 0.0063 REMARK 3 L TENSOR REMARK 3 L11: 0.0792 L22: 0.2817 REMARK 3 L33: 0.8886 L12: 0.1268 REMARK 3 L13: 0.2209 L23: 0.2831 REMARK 3 S TENSOR REMARK 3 S11: -0.0214 S12: -0.0021 S13: 0.0147 REMARK 3 S21: -0.0111 S22: -0.0508 S23: 0.0334 REMARK 3 S31: -0.0239 S32: 0.0390 S33: -0.2204 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN C REMARK 3 ORIGIN FOR THE GROUP (A): 15.7251 -16.8939 18.1511 REMARK 3 T TENSOR REMARK 3 T11: 0.5735 T22: 0.6742 REMARK 3 T33: 0.7807 T12: -0.0666 REMARK 3 T13: 0.0931 T23: -0.0304 REMARK 3 L TENSOR REMARK 3 L11: 0.0746 L22: 0.2099 REMARK 3 L33: 0.1818 L12: 0.0277 REMARK 3 L13: -0.0570 L23: -0.1101 REMARK 3 S TENSOR REMARK 3 S11: -0.0134 S12: -0.0267 S13: -0.0083 REMARK 3 S21: -0.0138 S22: -0.0426 S23: 0.0024 REMARK 3 S31: 0.0149 S32: 0.0388 S33: 0.0350 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 4HXJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000076044. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97885 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6468 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 29.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.17000 REMARK 200 R SYM (I) : 0.17000 REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : 0.36000 REMARK 200 R SYM FOR SHELL (I) : 0.36000 REMARK 200 FOR SHELL : 7.000 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: 1FMK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS, PH 8.0, 1.3M SODIUM REMARK 280 CITRATE, VAPOR DIFFUSION, HANGING 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 20.41500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 GLY B 82 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 GLY A 82 N CA REMARK 470 GLU A 93 CD OE1 OE2 REMARK 470 GLU A 97 CG CD OE1 OE2 REMARK 470 LYS A 103 CD CE NZ REMARK 470 LYS A 104 NZ REMARK 470 GLU A 115 CG CD OE1 OE2 REMARK 470 GLU B 93 CD OE1 OE2 REMARK 470 GLU B 115 CG CD OE1 OE2 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 THR A 96 -156.81 -143.44 REMARK 500 SER A 140 48.41 -153.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FMK RELATED DB: PDB DBREF 4HXJ A 84 141 UNP P12931 SRC_HUMAN 87 144 DBREF 4HXJ B 84 141 UNP P12931 SRC_HUMAN 87 144 DBREF 4HXJ C 760 762 UNP P05106 ITB3_HUMAN 786 788 SEQADV 4HXJ GLY A 82 UNP P12931 EXPRESSION TAG SEQADV 4HXJ SER A 83 UNP P12931 EXPRESSION TAG SEQADV 4HXJ GLY B 82 UNP P12931 EXPRESSION TAG SEQADV 4HXJ SER B 83 UNP P12931 EXPRESSION TAG SEQRES 1 A 60 GLY SER THR THR PHE VAL ALA LEU TYR ASP TYR GLU SER SEQRES 2 A 60 ARG THR 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 SER 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 SER THR THR PHE VAL ALA LEU TYR ASP TYR GLU SER SEQRES 2 B 60 ARG THR GLU THR ASP LEU SER PHE LYS LYS GLY GLU ARG SEQRES 3 B 60 LEU GLN ILE VAL ASN ASN THR GLU GLY ASP TRP TRP LEU SEQRES 4 B 60 ALA HIS SER LEU SER THR GLY GLN THR GLY TYR ILE PRO SEQRES 5 B 60 SER ASN TYR VAL ALA PRO SER ASP SEQRES 1 C 3 ARG GLY THR FORMUL 4 HOH *95(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 GLN A 109 -1 N GLN A 109 O HIS A 122 SHEET 4 A 5 THR A 85 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 SHEET 1 B 5 THR B 129 PRO B 133 0 SHEET 2 B 5 TRP B 118 SER B 123 -1 N ALA B 121 O GLY B 130 SHEET 3 B 5 ARG B 107 ASN B 112 -1 N GLN B 109 O HIS B 122 SHEET 4 B 5 PHE B 86 ALA B 88 -1 N PHE B 86 O LEU B 108 SHEET 5 B 5 VAL B 137 PRO B 139 -1 O ALA B 138 N VAL B 87 CRYST1 27.980 40.830 43.340 90.00 105.97 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 0.035740 0.000000 0.010228 0.00000 SCALE2 0.000000 0.024492 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024000 0.00000