HEADER SIGNALING PROTEIN 27-JUN-21 7R8X TITLE CRYSTAL STRUCTURE OF THE LNK SH2 DOMAIN IN COMPLEX WITH AN EPOR PY454 TITLE 2 PHOSPHOPEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SH2B ADAPTER PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 328-438; COMPND 5 SYNONYM: LYMPHOCYTE ADAPTER PROTEIN,LYMPHOCYTE-SPECIFIC ADAPTER COMPND 6 PROTEIN LNK,SIGNAL TRANSDUCTION PROTEIN LNK; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: EPOR PY454 PHOSPHOPEPTIDE; COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: SH2B3, LNK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS LNK, SH2B3, JAK/STAT, MPNS, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.MORRIS,N.J.KERSHAW,J.J.BABON REVDAT 4 15-NOV-23 7R8X 1 REMARK REVDAT 3 18-OCT-23 7R8X 1 REMARK REVDAT 2 03-NOV-21 7R8X 1 JRNL REVDAT 1 06-OCT-21 7R8X 0 JRNL AUTH R.MORRIS,Y.ZHANG,J.I.ELLYARD,C.G.VINUESA,J.M.MURPHY, JRNL AUTH 2 A.LAKTYUSHIN,N.J.KERSHAW,J.J.BABON JRNL TITL STRUCTURAL AND FUNCTIONAL ANALYSIS OF TARGET RECOGNITION BY JRNL TITL 2 THE LYMPHOCYTE ADAPTOR PROTEIN LNK. JRNL REF NAT COMMUN V. 12 6110 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 34671038 JRNL DOI 10.1038/S41467-021-26394-6 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 7314 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.710 REMARK 3 FREE R VALUE TEST SET COUNT : 710 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 33.9000 - 3.9300 1.00 1358 147 0.1558 0.1730 REMARK 3 2 3.9300 - 3.1200 1.00 1330 145 0.2019 0.2650 REMARK 3 3 3.1200 - 2.7300 1.00 1322 140 0.2624 0.2956 REMARK 3 4 2.7300 - 2.4800 1.00 1305 133 0.2499 0.3099 REMARK 3 5 2.4800 - 2.3000 0.99 1289 145 0.2855 0.3241 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) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.290 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 53.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.82 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 7R8X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1000257739. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.953740 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7318 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 33.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : 0.04408 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.49240 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.810 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 2HDV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG8000, 0.05 M MAGNESIUM ACETATE, REMARK 280 0.1 M TRIS, PH 8.5, PH 9.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 12.68400 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 25.36800 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.02600 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 31.71000 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 6.34200 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: 1150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 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 ASP A 328 CG OD1 OD2 REMARK 470 ARG A 369 CZ NH1 NH2 REMARK 470 ARG A 370 CD NE CZ NH1 NH2 REMARK 470 ARG A 382 CD NE CZ NH1 NH2 REMARK 470 ARG A 387 CZ NH1 NH2 REMARK 470 GLU A 392 CG CD OE1 OE2 REMARK 470 ARG A 393 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 395 CG CD OE1 NE2 REMARK 470 ARG A 397 CD NE CZ NH1 NH2 REMARK 470 ARG A 411 CZ NH1 NH2 REMARK 470 ARG A 429 CZ NH1 NH2 REMARK 470 SER A 438 OG REMARK 470 LYS C 453 CE NZ REMARK 470 SER C 460 OG 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 PRO A 340 40.70 -94.99 REMARK 500 ARG A 369 76.50 -116.09 REMARK 500 GLN A 399 -117.57 56.54 REMARK 500 SER A 431 -110.95 -105.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7R8W RELATED DB: PDB DBREF 7R8X A 328 438 UNP O09039 SH2B3_MOUSE 328 438 DBREF 7R8X C 453 460 PDB 7R8X 7R8X 453 460 SEQRES 1 A 111 ASP HIS PHE LEU SER CYS TYR PRO TRP PHE HIS GLY PRO SEQRES 2 A 111 ILE SER ARG VAL ARG ALA ALA GLN LEU VAL GLN LEU GLN SEQRES 3 A 111 GLY PRO ASP ALA HIS GLY VAL PHE LEU VAL ARG GLN SER SEQRES 4 A 111 GLU SER ARG ARG GLY GLU TYR VAL LEU THR PHE ASN LEU SEQRES 5 A 111 GLN GLY ARG ALA LYS HIS LEU ARG LEU VAL LEU THR GLU SEQRES 6 A 111 ARG GLY GLN CYS ARG VAL GLN HIS LEU HIS PHE PRO SER SEQRES 7 A 111 VAL VAL ASP MET LEU ARG HIS PHE GLN ARG SER PRO ILE SEQRES 8 A 111 PRO LEU GLU CYS GLY ALA ALA CYS ASP VAL ARG LEU SER SEQRES 9 A 111 GLY TYR VAL VAL VAL LEU SER SEQRES 1 C 8 LYS PTR LEU TYR LEU VAL VAL SER HET PTR C 454 16 HETNAM PTR O-PHOSPHOTYROSINE HETSYN PTR PHOSPHONOTYROSINE FORMUL 2 PTR C9 H12 N O6 P FORMUL 3 HOH *13(H2 O) HELIX 1 AA1 HIS A 329 TYR A 334 5 6 HELIX 2 AA2 SER A 342 LEU A 352 1 11 HELIX 3 AA3 GLN A 353 HIS A 358 5 6 HELIX 4 AA4 SER A 405 SER A 416 1 12 HELIX 5 AA5 CYS A 422 ASP A 427 5 6 SHEET 1 AA1 5 PHE A 361 GLN A 365 0 SHEET 2 AA1 5 TYR A 373 LEU A 379 -1 O VAL A 374 N ARG A 364 SHEET 3 AA1 5 ARG A 382 LEU A 390 -1 O ARG A 382 N LEU A 379 SHEET 4 AA1 5 CYS A 396 VAL A 398 -1 O ARG A 397 N VAL A 389 SHEET 5 AA1 5 LEU A 401 PHE A 403 -1 O LEU A 401 N VAL A 398 SSBOND 1 CYS A 422 CYS A 426 1555 1555 2.03 LINK C LYS C 453 N PTR C 454 1555 1555 1.33 LINK C PTR C 454 N LEU C 455 1555 1555 1.33 CRYST1 86.157 86.157 38.052 90.00 90.00 120.00 P 61 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 0.011607 0.006701 0.000000 0.00000 SCALE2 0.000000 0.013402 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026280 0.00000