HEADER PROTEIN BINDING 26-JAN-20 6XX4 TITLE CRYSTAL STRUCTURE OF THE C-SRC SH3 DOMAIN H122R-Q128E MUTANT IN TITLE 2 COMPLEX WITH NI(II) AT PH 7.5 CO-CRYSTALLIZED WITH METHYL BETA- TITLE 3 CYCLODEXTRIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTO-ONCOGENE C-SRC,PP60C-SRC,P60-SRC; COMPND 5 EC: 2.7.10.2; COMPND 6 ENGINEERED: YES; COMPND 7 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: PHTP1 KEYWDS BETA BARREL, SH3 DOMAIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR A.CAMARA-ARTIGAS REVDAT 4 24-JAN-24 6XX4 1 HETSYN REVDAT 3 29-JUL-20 6XX4 1 COMPND REMARK HET HETNAM REVDAT 3 2 1 HETSYN FORMUL LINK SITE REVDAT 3 3 1 ATOM REVDAT 2 03-JUN-20 6XX4 1 JRNL REVDAT 1 22-APR-20 6XX4 0 JRNL AUTH M.PLAZA-GARRIDO,M.C.SALINAS-GARCIA,J.C.MARTINEZ, JRNL AUTH 2 A.CAMARA-ARTIGAS JRNL TITL THE EFFECT OF AN ENGINEERED ATCUN MOTIF ON THE STRUCTURE AND JRNL TITL 2 BIOPHYSICAL PROPERTIES OF THE SH3 DOMAIN OF C-SRC TYROSINE JRNL TITL 3 KINASE. JRNL REF J.BIOL.INORG.CHEM. V. 25 621 2020 JRNL REFN ESSN 1432-1327 JRNL PMID 32279137 JRNL DOI 10.1007/S00775-020-01785-0 REMARK 2 REMARK 2 RESOLUTION. 1.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1 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) : 1.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.240 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 53538 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 2695 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 28.7990 - 2.8011 0.98 2670 114 0.1989 0.2327 REMARK 3 2 2.8011 - 2.2236 1.00 2644 144 0.1918 0.1998 REMARK 3 3 2.2236 - 1.9426 1.00 2723 136 0.1465 0.1625 REMARK 3 4 1.9426 - 1.7650 1.00 2655 138 0.1453 0.1587 REMARK 3 5 1.7650 - 1.6385 1.00 2681 164 0.1411 0.1715 REMARK 3 6 1.6385 - 1.5419 1.00 2628 145 0.1361 0.1680 REMARK 3 7 1.5419 - 1.4647 1.00 2726 151 0.1316 0.1260 REMARK 3 8 1.4647 - 1.4009 1.00 2639 160 0.1353 0.1297 REMARK 3 9 1.4009 - 1.3470 1.00 2701 137 0.1284 0.1606 REMARK 3 10 1.3470 - 1.3005 1.00 2691 124 0.1354 0.1753 REMARK 3 11 1.3005 - 1.2599 1.00 2674 146 0.1303 0.1477 REMARK 3 12 1.2599 - 1.2238 1.00 2661 130 0.1374 0.1599 REMARK 3 13 1.2238 - 1.1916 1.00 2704 138 0.1361 0.1608 REMARK 3 14 1.1916 - 1.1626 1.00 2693 131 0.1351 0.1359 REMARK 3 15 1.1626 - 1.1361 1.00 2618 166 0.1319 0.1593 REMARK 3 16 1.1361 - 1.1119 1.00 2713 137 0.1507 0.1646 REMARK 3 17 1.1119 - 1.0897 1.00 2690 139 0.1696 0.2509 REMARK 3 18 1.0897 - 1.0691 1.00 2631 162 0.1932 0.2178 REMARK 3 19 1.0691 - 1.0500 1.00 2701 133 0.2196 0.2404 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) : 15.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.42 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6XX4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1292106476. 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) : 0.979464 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.1.30 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53538 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.050 REMARK 200 RESOLUTION RANGE LOW (A) : 30.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.48700 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: 4JZ4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4 M AMMONIUM SULFATE, 0.1 HEPES, 5 REMARK 280 MM NICKEL CHLORIDE, 10% GLYCEROL, 10MM METHYL BETA-CYCLODEXTRIN, REMARK 280 PH 7.5, VAPOR DIFFUSION, SITTING 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 27.04267 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 54.08533 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 54.08533 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 27.04267 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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 ASN A 112 REMARK 465 ASN A 113 REMARK 465 THR A 114 REMARK 465 GLU A 115 REMARK 465 GLY A 116 REMARK 465 ASP A 141 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 93 CG CD OE1 OE2 REMARK 470 GLU A 97 CG CD OE1 OE2 REMARK 470 LYS A 103 CG CD CE NZ REMARK 470 VAL A 111 CG1 CG2 REMARK 470 ASP A 117 CG OD1 OD2 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 -1.40 -173.67 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 GLY A 81 N REMARK 620 2 SER A 82 N 80.2 REMARK 620 3 HIS A 83 N 159.5 79.5 REMARK 620 4 HIS A 83 ND1 98.8 178.7 101.4 REMARK 620 N 1 2 3 DBREF 6XX4 A 85 141 UNP P00523 SRC_CHICK 85 141 SEQADV 6XX4 GLY A 81 UNP P00523 EXPRESSION TAG SEQADV 6XX4 SER A 82 UNP P00523 EXPRESSION TAG SEQADV 6XX4 HIS A 83 UNP P00523 EXPRESSION TAG SEQADV 6XX4 MET A 84 UNP P00523 EXPRESSION TAG SEQADV 6XX4 ARG A 122 UNP P00523 HIS 122 ENGINEERED MUTATION SEQADV 6XX4 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 ARG SER LEU THR THR GLY GLU THR GLY TYR ILE SEQRES 5 A 61 PRO SER ASN TYR VAL ALA PRO SER ASP HET ZB1 B 1 24 HET GLC B 2 21 HET GLC B 3 21 HET ZB2 B 4 24 HET ZB3 B 5 27 HET ZB2 B 6 24 HET ZB0 B 7 27 HET NI A 201 1 HETNAM ZB1 3-O-METHYL-ALPHA-D-GLUCOPYRANOSE HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM ZB2 2-O-METHYL-ALPHA-D-GLUCOPYRANOSE HETNAM ZB3 2,6-DI-O-METHYL-ALPHA-D-GLUCOPYRANOSE HETNAM ZB0 2,3-DI-O-METHYL-ALPHA-D-GLUCOPYRANOSE HETNAM NI NICKEL (II) ION HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 2 ZB1 C7 H14 O6 FORMUL 2 GLC 2(C6 H12 O6) FORMUL 2 ZB2 2(C7 H14 O6) FORMUL 2 ZB3 C8 H16 O6 FORMUL 2 ZB0 C8 H16 O6 FORMUL 3 NI NI 2+ FORMUL 4 HOH *37(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 ILE A 110 -1 N GLN A 109 O ARG 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 LINK O4 ZB1 B 1 C1 GLC B 2 1555 1555 1.38 LINK C1 ZB1 B 1 O4 ZB0 B 7 1555 1555 1.44 LINK O4 GLC B 2 C1 GLC B 3 1555 1555 1.42 LINK O4 GLC B 3 C1 ZB2 B 4 1555 1555 1.40 LINK O4 ZB2 B 4 C1 ZB3 B 5 1555 1555 1.40 LINK O4 ZB3 B 5 C1 ZB2 B 6 1555 1555 1.42 LINK O4 ZB2 B 6 C1 ZB0 B 7 1555 1555 1.43 LINK N GLY A 81 NI NI A 201 1555 1555 1.87 LINK N SER A 82 NI NI A 201 1555 1555 2.01 LINK N HIS A 83 NI NI A 201 1555 1555 1.98 LINK ND1 HIS A 83 NI NI A 201 1555 1555 1.94 CRYST1 35.571 35.571 81.128 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 0.028113 0.016231 0.000000 0.00000 SCALE2 0.000000 0.032462 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012326 0.00000