HEADER PROTEIN BINDING 16-NOV-14 4RTZ TITLE CRYSTAL STRUCTURE OF THE C-SRC-SH3 DOMAIN IN COMPLEX WITH THE HIGH TITLE 2 AFFINITY PEPTIDE VSL12 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SH3 DOMAIN (UNP RESIDUES 85-141); COMPND 5 SYNONYM: 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: VSL12 PEPTIDE; COMPND 10 CHAIN: B; COMPND 11 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 ORGANISM_TAXID: 32630; SOURCE 14 OTHER_DETAILS: SYNTHETIC HIGH AFFINITY PEPTIDE KEYWDS BETA SHANDWICH, SH3 DOMAIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR A.CAMARA-ARTIGAS,J.BACARIZO REVDAT 1 28-OCT-15 4RTZ 0 JRNL AUTH A.CAMARA-ARTIGAS JRNL TITL CRYSTAL STRUCTURE OF THE C-SRC-SH3 DOMAIN IN COMPLEX WITH JRNL TITL 2 THE HIGH AFFINITY PEPTIDE VSL12 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 0.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 65154 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.143 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.158 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3256 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 30.0490 - 2.7837 0.98 2700 134 0.1413 0.1469 REMARK 3 2 2.7837 - 2.2097 0.98 2670 168 0.1465 0.1794 REMARK 3 3 2.2097 - 1.9305 0.99 2701 161 0.1290 0.1360 REMARK 3 4 1.9305 - 1.7540 0.99 2736 119 0.1287 0.1607 REMARK 3 5 1.7540 - 1.6283 0.98 2711 129 0.1265 0.2007 REMARK 3 6 1.6283 - 1.5323 0.99 2707 176 0.1250 0.1396 REMARK 3 7 1.5323 - 1.4556 1.00 2727 161 0.1172 0.1130 REMARK 3 8 1.4556 - 1.3922 1.00 2738 124 0.1185 0.1314 REMARK 3 9 1.3922 - 1.3386 1.00 2762 120 0.1211 0.1382 REMARK 3 10 1.3386 - 1.2924 0.99 2699 152 0.1258 0.1514 REMARK 3 11 1.2924 - 1.2520 0.99 2711 142 0.1301 0.1455 REMARK 3 12 1.2520 - 1.2162 0.99 2746 148 0.1287 0.1519 REMARK 3 13 1.2162 - 1.1842 0.99 2681 171 0.1329 0.1539 REMARK 3 14 1.1842 - 1.1553 0.99 2700 157 0.1386 0.1444 REMARK 3 15 1.1553 - 1.1290 0.98 2683 127 0.1445 0.1621 REMARK 3 16 1.1290 - 1.1050 0.99 2681 144 0.1566 0.1573 REMARK 3 17 1.1050 - 1.0829 0.99 2747 147 0.1734 0.1609 REMARK 3 18 1.0829 - 1.0625 0.98 2668 137 0.1812 0.2005 REMARK 3 19 1.0625 - 1.0435 0.98 2705 134 0.2151 0.2250 REMARK 3 20 1.0435 - 1.0258 0.98 2635 137 0.2452 0.2377 REMARK 3 21 1.0258 - 1.0092 0.96 2686 133 0.2847 0.3014 REMARK 3 22 1.0092 - 0.9937 0.97 2652 123 0.3071 0.2678 REMARK 3 23 0.9937 - 0.9791 0.88 2452 112 0.3120 0.2898 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) : 15.710 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.43 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.67 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 : 0.009 591 REMARK 3 ANGLE : 1.381 811 REMARK 3 CHIRALITY : 0.083 87 REMARK 3 PLANARITY : 0.007 106 REMARK 3 DIHEDRAL : 11.098 216 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 4RTZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-NOV-14. REMARK 100 THE RCSB ID CODE IS RCSB087793. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.979491 REMARK 200 MONOCHROMATOR : CHANNEL-CUT MONOCHROMATOR AND A REMARK 200 KIRKPATRICK-BAEZ (KB) FOCUSING REMARK 200 SYSTEM REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34334 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.980 REMARK 200 RESOLUTION RANGE LOW (A) : 41.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.83600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 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: 4JZ4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.7 M AMMONIUM SULPHATE, 0.1 M HEPES, REMARK 280 5 MM NICL2 AND 10% GLYCEROL, PH 7.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 16.45200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.03300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.52300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.03300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.45200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.52300 REMARK 290 SMTRY3 4 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4400 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 VAL B 1 REMARK 465 SER B 2 REMARK 465 LEU B 3 REMARK 465 ALA B 4 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 ARG B 5 CG CD NE CZ NH1 NH2 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 82 -2.52 -168.52 REMARK 500 REMARK 500 REMARK: NULL 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 NI A 201 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 82 N REMARK 620 2 HIS A 83 N 83.6 REMARK 620 3 GLY A 81 N 85.9 169.3 REMARK 620 4 HIS A 83 ND1 174.1 95.0 95.7 REMARK 620 N 1 2 3 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4RTU RELATED DB: PDB REMARK 900 RELATED ID: 4RTV RELATED DB: PDB REMARK 900 RELATED ID: 4RTW RELATED DB: PDB REMARK 900 RELATED ID: 4RTX RELATED DB: PDB REMARK 900 RELATED ID: 4RTY RELATED DB: PDB DBREF 4RTZ A 85 141 UNP P00523 SRC_CHICK 85 141 DBREF 4RTZ B 1 12 PDB 4RTZ 4RTZ 1 12 SEQADV 4RTZ GLY A 81 UNP P00523 EXPRESSION TAG SEQADV 4RTZ SER A 82 UNP P00523 EXPRESSION TAG SEQADV 4RTZ HIS A 83 UNP P00523 EXPRESSION TAG SEQADV 4RTZ MET A 84 UNP P00523 EXPRESSION TAG 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 GLN THR GLY TYR ILE SEQRES 5 A 61 PRO SER ASN TYR VAL ALA PRO SER ASP SEQRES 1 B 12 VAL SER LEU ALA ARG ARG PRO LEU PRO PRO LEU PRO HET NI A 201 1 HET GOL A 202 14 HETNAM NI NICKEL (II) ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 NI NI 2+ FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *62(H2 O) HELIX 1 1 SER A 134 TYR A 136 5 3 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 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 LINK N SER A 82 NI NI A 201 1555 1555 1.84 LINK N HIS A 83 NI NI A 201 1555 1555 1.89 LINK N GLY A 81 NI NI A 201 1555 1555 1.90 LINK ND1 HIS A 83 NI NI A 201 1555 1555 1.91 SITE 1 AC1 3 GLY A 81 SER A 82 HIS A 83 SITE 1 AC2 5 THR A 98 LEU A 120 SER A 140 ASP A 141 SITE 2 AC2 5 HOH A 338 CRYST1 32.904 41.046 44.066 90.00 90.00 90.00 P 21 21 21 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 0.030391 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024363 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022693 0.00000 MASTER 286 0 2 1 5 0 3 6 0 0 0 6 END