HEADER SIGNALING PROTEIN 09-MAR-18 6FXF TITLE CRYSTAL STRUCTURE OF THE SAM DOMAIN OF MURINE SLY1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SAM AND SH3 DOMAIN-CONTAINING PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SH3 PROTEIN EXPRESSED IN LYMPHOCYTES; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: SASH3, SLY; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS SLY1, SAM, ADAPTER PROTEIN, SCAFFOLD PROTEIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.K.KUKUK,J.GRANZIN,R.BATRA-SAFFERLING,B.W.KOENIG REVDAT 2 17-JAN-24 6FXF 1 REMARK REVDAT 1 30-JAN-19 6FXF 0 JRNL AUTH L.KUKUK,A.J.DINGLEY,J.GRANZIN,L.NAGEL-STEGER, JRNL AUTH 2 P.THIAGARAJAN-ROSENKRANZ,D.CIUPKA,K.HANEL, JRNL AUTH 3 R.BATRA-SAFFERLING,V.PACHECO,M.STOLDT,K.PFEFFER, JRNL AUTH 4 S.BEER-HAMMER,D.WILLBOLD,B.W.KOENIG JRNL TITL STRUCTURE OF THE SLY1 SAM HOMODIMER REVEALS A NEW INTERFACE JRNL TITL 2 FOR SAM DOMAIN SELF-ASSOCIATION. JRNL REF SCI REP V. 9 54 2019 JRNL REFN ESSN 2045-2322 JRNL PMID 30631134 JRNL DOI 10.1038/S41598-018-37185-3 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 6319 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 319 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 39.9752 - 2.5831 1.00 3100 146 0.2004 0.2176 REMARK 3 2 2.5831 - 2.0503 1.00 2900 173 0.2991 0.3386 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 1.00 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.570 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 55.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 65.05 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 : 0.007 546 REMARK 3 ANGLE : 0.960 740 REMARK 3 CHIRALITY : 0.040 87 REMARK 3 PLANARITY : 0.004 96 REMARK 3 DIHEDRAL : 13.263 337 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESID 253 THROUGH 276 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.7549 -8.7567 -17.4925 REMARK 3 T TENSOR REMARK 3 T11: 0.3844 T22: 0.7742 REMARK 3 T33: 0.5194 T12: -0.0671 REMARK 3 T13: -0.0292 T23: 0.1848 REMARK 3 L TENSOR REMARK 3 L11: 4.2291 L22: 3.4749 REMARK 3 L33: 0.9568 L12: -1.5002 REMARK 3 L13: -1.8657 L23: 1.3360 REMARK 3 S TENSOR REMARK 3 S11: -0.0639 S12: 0.3815 S13: -0.5789 REMARK 3 S21: -0.0311 S22: 0.2739 S23: 0.7302 REMARK 3 S31: -0.0022 S32: -1.3616 S33: -0.0657 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESID 277 THROUGH 286 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.7247 -0.7863 -10.6475 REMARK 3 T TENSOR REMARK 3 T11: 0.6262 T22: 0.6316 REMARK 3 T33: 0.5836 T12: -0.0565 REMARK 3 T13: 0.1341 T23: 0.1044 REMARK 3 L TENSOR REMARK 3 L11: 8.1231 L22: 6.0546 REMARK 3 L33: 2.9956 L12: -0.2057 REMARK 3 L13: -2.0982 L23: -1.3307 REMARK 3 S TENSOR REMARK 3 S11: 0.8925 S12: -1.2023 S13: 1.9947 REMARK 3 S21: 2.1001 S22: 0.2294 S23: 0.6143 REMARK 3 S31: -1.2307 S32: -0.9330 S33: -1.0447 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND (RESID 287 THROUGH 294 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.3252 -5.4044 -9.0771 REMARK 3 T TENSOR REMARK 3 T11: 0.4716 T22: 0.9545 REMARK 3 T33: 0.6782 T12: 0.0065 REMARK 3 T13: -0.0756 T23: -0.0149 REMARK 3 L TENSOR REMARK 3 L11: 7.4243 L22: 3.8080 REMARK 3 L33: 9.2397 L12: -5.2779 REMARK 3 L13: -0.3153 L23: -0.4378 REMARK 3 S TENSOR REMARK 3 S11: -0.0691 S12: -1.7951 S13: 0.3862 REMARK 3 S21: 1.1885 S22: 0.3461 S23: -0.9039 REMARK 3 S31: -0.8699 S32: 1.1113 S33: -0.6259 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND (RESID 295 THROUGH 317 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.8605 -3.6017 -18.0225 REMARK 3 T TENSOR REMARK 3 T11: 0.4275 T22: 0.5344 REMARK 3 T33: 0.4937 T12: -0.0422 REMARK 3 T13: 0.1249 T23: 0.1688 REMARK 3 L TENSOR REMARK 3 L11: 4.6991 L22: 9.0524 REMARK 3 L33: 6.7017 L12: 1.3690 REMARK 3 L13: -0.9915 L23: -1.0489 REMARK 3 S TENSOR REMARK 3 S11: 0.2200 S12: -0.9424 S13: 0.4822 REMARK 3 S21: -0.2270 S22: 0.5832 S23: -0.5683 REMARK 3 S31: -0.7369 S32: 0.2532 S33: -0.5347 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 6FXF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1200009087. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9677 REMARK 200 MONOCHROMATOR : SI (111) MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6358 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 47.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1V38 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M K2HPO4, 2.2 M (NH4)2SO4, 0.1 M REMARK 280 NACL, 0.1 M IMIDAZOLE, PH 8, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 47.33700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 22.04450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 22.04450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 23.66850 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 22.04450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 22.04450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 71.00550 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 22.04450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 22.04450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 23.66850 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 22.04450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 22.04450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 71.00550 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 47.33700 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: 1730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -47.33700 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 255 CG CD CE NZ REMARK 480 GLU A 286 CG CD OE1 OE2 REMARK 480 TYR A 316 CE1 CE2 CZ OH DBREF 6FXF A 254 317 UNP Q8K352 SASH3_MOUSE 254 317 SEQADV 6FXF GLY A 253 UNP Q8K352 EXPRESSION TAG SEQRES 1 A 65 GLY PRO LYS THR LEU HIS GLU LEU LEU GLU ARG ILE GLY SEQRES 2 A 65 LEU GLU GLU HIS THR SER THR LEU LEU LEU ASN GLY TYR SEQRES 3 A 65 GLN THR LEU GLU ASP PHE LYS GLU LEU ARG GLU THR HIS SEQRES 4 A 65 LEU ASN GLU LEU ASN ILE MET ASP PRO GLN HIS ARG ALA SEQRES 5 A 65 LYS LEU LEU THR ALA ALA GLU LEU LEU LEU ASP TYR ASP FORMUL 2 HOH *10(H2 O) HELIX 1 AA1 THR A 256 ILE A 264 1 9 HELIX 2 AA2 LEU A 266 GLU A 268 5 3 HELIX 3 AA3 HIS A 269 ASN A 276 1 8 HELIX 4 AA4 THR A 280 LYS A 285 1 6 HELIX 5 AA5 ARG A 288 LEU A 295 1 8 HELIX 6 AA6 ASP A 299 ASP A 317 1 19 CRYST1 44.089 44.089 94.674 90.00 90.00 90.00 P 41 21 2 8 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 0.022681 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022681 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010563 0.00000