HEADER TRANSFERASE 10-JUL-14 4TZI TITLE STRUCTURE OF UNLIGANDED LYN SH2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN KINASE LYN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SH2 DOMAIN RESIDUES 115-229; COMPND 5 SYNONYM: V-YES-1 YAMAGUCHI SARCOMA VIRAL RELATED ONCOGENE HOMOLOG, COMPND 6 P53LYN,P56LYN; COMPND 7 EC: 2.7.10.2; COMPND 8 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: LYN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SH2 DOMAIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR L.E.WYBENGA-GROOT REVDAT 5 27-SEP-23 4TZI 1 REMARK REVDAT 4 22-NOV-17 4TZI 1 SOURCE REMARK REVDAT 3 01-APR-15 4TZI 1 JRNL REVDAT 2 11-FEB-15 4TZI 1 JRNL REVDAT 1 21-JAN-15 4TZI 0 JRNL AUTH L.L.JIN,L.E.WYBENGA-GROOT,J.TONG,P.TAYLOR,M.D.MINDEN, JRNL AUTH 2 S.TRUDEL,C.J.MCGLADE,M.F.MORAN JRNL TITL TYROSINE PHOSPHORYLATION OF THE LYN SRC HOMOLOGY 2 (SH2) JRNL TITL 2 DOMAIN MODULATES ITS BINDING AFFINITY AND SPECIFICITY. JRNL REF MOL.CELL PROTEOMICS V. 14 695 2015 JRNL REFN ESSN 1535-9484 JRNL PMID 25587033 JRNL DOI 10.1074/MCP.M114.044404 REMARK 2 REMARK 2 RESOLUTION. 2.10 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-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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 13919 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.630 REMARK 3 FREE R VALUE TEST SET COUNT : 1062 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 32.7603 - 4.1979 1.00 1682 146 0.1778 0.2248 REMARK 3 2 4.1979 - 3.3330 1.00 1627 127 0.1766 0.2261 REMARK 3 3 3.3330 - 2.9120 1.00 1611 134 0.2129 0.2878 REMARK 3 4 2.9120 - 2.6459 1.00 1599 130 0.2223 0.2712 REMARK 3 5 2.6459 - 2.4563 1.00 1603 113 0.2227 0.3017 REMARK 3 6 2.4563 - 2.3115 1.00 1536 153 0.2259 0.3023 REMARK 3 7 2.3115 - 2.1958 1.00 1577 144 0.2281 0.2554 REMARK 3 8 2.1958 - 2.1000 1.00 1622 115 0.2112 0.2677 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.570 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.53 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.86 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 1749 REMARK 3 ANGLE : 1.093 2355 REMARK 3 CHIRALITY : 0.044 254 REMARK 3 PLANARITY : 0.005 303 REMARK 3 DIHEDRAL : 12.882 647 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 27.2063 32.3366 19.0802 REMARK 3 T TENSOR REMARK 3 T11: 0.2191 T22: 0.1984 REMARK 3 T33: 0.1892 T12: -0.0718 REMARK 3 T13: -0.0309 T23: -0.0001 REMARK 3 L TENSOR REMARK 3 L11: 0.4052 L22: 0.8408 REMARK 3 L33: 2.1605 L12: -0.2001 REMARK 3 L13: -0.4440 L23: -1.3900 REMARK 3 S TENSOR REMARK 3 S11: 0.0171 S12: 0.0868 S13: -0.0091 REMARK 3 S21: -0.0334 S22: -0.0897 S23: -0.0198 REMARK 3 S31: -0.0320 S32: 0.1838 S33: 0.0059 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 4TZI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1000202524. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : VARIMAX VHF REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13934 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.09200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 10.20 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: 3HCK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 UL SEED STOCK WITH 0.2 UL WELL REMARK 280 SOLUTION (0.1 M TRIS PH 8.5, 20% V/V ETHANOL) AND 0.3 UL OF REMARK 280 PROTEIN (20 MM HEPES PH 7.0, 150 MM NACL, 1 MM DTT, 22.5 MG/ML), REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 55.95750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 13.99750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 55.95750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 13.99750 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 SER A 115 REMARK 465 ASN A 116 REMARK 465 TYR A 117 REMARK 465 VAL A 118 REMARK 465 PRO A 229 REMARK 465 SER B 115 REMARK 465 ASN B 116 REMARK 465 TYR B 117 REMARK 465 VAL B 118 REMARK 465 ALA B 119 REMARK 465 ASN B 190 REMARK 465 PRO B 229 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 LYS A 120 CG CD CE NZ REMARK 470 LYS A 132 CG CD CE NZ REMARK 470 LYS A 137 CG CD CE NZ REMARK 470 ASP A 189 CG OD1 OD2 REMARK 470 ASN A 190 CG OD1 ND2 REMARK 470 LYS B 120 CG CD CE NZ REMARK 470 GLU B 125 CG CD OE1 OE2 REMARK 470 LYS B 137 CG CD CE NZ REMARK 470 ARG B 141 CG CD NE CZ NH1 NH2 REMARK 470 LEU B 188 CG CD1 CD2 REMARK 470 ASP B 189 CG OD1 OD2 REMARK 470 ILE B 227 CG1 CG2 CD1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 355 O HOH A 358 2.10 REMARK 500 O HOH A 323 O HOH A 329 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 LYS A 120 86.87 -158.91 REMARK 500 VAL A 121 -60.93 71.43 REMARK 500 GLU A 223 -88.33 -117.33 REMARK 500 SER B 158 152.99 -49.51 REMARK 500 GLU B 223 -107.52 -113.35 REMARK 500 REMARK 500 REMARK: NULL DBREF 4TZI A 115 229 UNP P25911 LYN_MOUSE 115 229 DBREF 4TZI B 115 229 UNP P25911 LYN_MOUSE 115 229 SEQRES 1 A 115 SER ASN TYR VAL ALA LYS VAL ASN THR LEU GLU THR GLU SEQRES 2 A 115 GLU TRP PHE PHE LYS ASP ILE THR ARG LYS ASP ALA GLU SEQRES 3 A 115 ARG GLN LEU LEU ALA PRO GLY ASN SER ALA GLY ALA PHE SEQRES 4 A 115 LEU ILE ARG GLU SER GLU THR LEU LYS GLY SER PHE SER SEQRES 5 A 115 LEU SER VAL ARG ASP TYR ASP PRO MET HIS GLY ASP VAL SEQRES 6 A 115 ILE LYS HIS TYR LYS ILE ARG SER LEU ASP ASN GLY GLY SEQRES 7 A 115 TYR TYR ILE SER PRO ARG ILE THR PHE PRO CYS ILE SER SEQRES 8 A 115 ASP MET ILE LYS HIS TYR GLN LYS GLN SER ASP GLY LEU SEQRES 9 A 115 CYS ARG ARG LEU GLU LYS ALA CYS ILE SER PRO SEQRES 1 B 115 SER ASN TYR VAL ALA LYS VAL ASN THR LEU GLU THR GLU SEQRES 2 B 115 GLU TRP PHE PHE LYS ASP ILE THR ARG LYS ASP ALA GLU SEQRES 3 B 115 ARG GLN LEU LEU ALA PRO GLY ASN SER ALA GLY ALA PHE SEQRES 4 B 115 LEU ILE ARG GLU SER GLU THR LEU LYS GLY SER PHE SER SEQRES 5 B 115 LEU SER VAL ARG ASP TYR ASP PRO MET HIS GLY ASP VAL SEQRES 6 B 115 ILE LYS HIS TYR LYS ILE ARG SER LEU ASP ASN GLY GLY SEQRES 7 B 115 TYR TYR ILE SER PRO ARG ILE THR PHE PRO CYS ILE SER SEQRES 8 B 115 ASP MET ILE LYS HIS TYR GLN LYS GLN SER ASP GLY LEU SEQRES 9 B 115 CYS ARG ARG LEU GLU LYS ALA CYS ILE SER PRO FORMUL 3 HOH *105(H2 O) HELIX 1 AA1 THR A 135 LEU A 144 1 10 HELIX 2 AA2 CYS A 203 GLN A 214 1 12 HELIX 3 AA3 THR B 123 GLU B 127 5 5 HELIX 4 AA4 THR B 135 ALA B 145 1 11 HELIX 5 AA5 CYS B 203 GLN B 214 1 12 SHEET 1 AA1 5 PHE A 153 GLU A 157 0 SHEET 2 AA1 5 PHE A 165 TYR A 172 -1 O SER A 168 N LEU A 154 SHEET 3 AA1 5 ASP A 178 SER A 187 -1 O LYS A 181 N VAL A 169 SHEET 4 AA1 5 TYR A 193 SER A 196 -1 O TYR A 194 N ARG A 186 SHEET 5 AA1 5 ILE A 199 PHE A 201 -1 O PHE A 201 N TYR A 193 SHEET 1 AA2 3 PHE B 153 GLU B 157 0 SHEET 2 AA2 3 PHE B 165 ASP B 173 -1 O SER B 168 N LEU B 154 SHEET 3 AA2 3 GLY B 177 ILE B 185 -1 O VAL B 179 N ASP B 171 CISPEP 1 LYS A 120 VAL A 121 0 0.51 CRYST1 111.915 27.995 74.915 90.00 96.81 90.00 C 1 2 1 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 0.008935 0.000000 0.001068 0.00000 SCALE2 0.000000 0.035721 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013443 0.00000