HEADER SIGNALING PROTEIN 25-OCT-22 8EXI TITLE CRYSTAL STRUCTURE OF APO PTP1B D181A/Q262A PHOSPHATASE DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN-TYROSINE PHOSPHATASE 1B,PTP-1B; COMPND 5 EC: 3.1.3.48; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PTPN1, PTP1B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PTP1B, JAK/STAT, IRK, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.MORRIS,N.J.KERSHAW,J.J.BABON REVDAT 2 25-OCT-23 8EXI 1 REMARK REVDAT 1 05-JUL-23 8EXI 0 JRNL AUTH R.MORRIS,N.KEATING,C.TAN,H.CHEN,A.LAKTYUSHIN,T.SAIYED, JRNL AUTH 2 N.P.D.LIAU,N.A.NICOLA,T.TIGANIS,N.J.KERSHAW,J.J.BABON JRNL TITL STRUCTURE GUIDED STUDIES OF THE INTERACTION BETWEEN PTP1B JRNL TITL 2 AND JAK. JRNL REF COMMUN BIOL V. 6 641 2023 JRNL REFN ESSN 2399-3642 JRNL PMID 37316570 JRNL DOI 10.1038/S42003-023-05020-9 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 63292 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.150 REMARK 3 FREE R VALUE TEST SET COUNT : 1991 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 44.3600 - 3.8532 1.00 4609 150 0.1584 0.1856 REMARK 3 2 3.8532 - 3.0586 1.00 4453 142 0.1812 0.1857 REMARK 3 3 3.0586 - 2.6720 1.00 4421 146 0.2026 0.2321 REMARK 3 4 2.6720 - 2.4277 1.00 4405 146 0.1977 0.2279 REMARK 3 5 2.4277 - 2.2537 1.00 4356 144 0.2049 0.2149 REMARK 3 6 2.2537 - 2.1209 1.00 4381 142 0.1989 0.2137 REMARK 3 7 2.1209 - 2.0146 1.00 4333 144 0.2115 0.2587 REMARK 3 8 2.0146 - 1.9269 1.00 4362 139 0.2083 0.2572 REMARK 3 9 1.9269 - 1.8528 1.00 4360 138 0.2122 0.2097 REMARK 3 10 1.8528 - 1.7888 1.00 4342 140 0.2200 0.2496 REMARK 3 11 1.7888 - 1.7329 1.00 4345 140 0.2433 0.2891 REMARK 3 12 1.7329 - 1.6834 1.00 4337 139 0.2706 0.3032 REMARK 3 13 1.6834 - 1.6390 1.00 4311 140 0.2662 0.2719 REMARK 3 14 1.6390 - 1.5990 0.98 4286 141 0.2786 0.3068 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.75 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 8EXI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1000266600. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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) : 0.95373 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 : 63299 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.599 REMARK 200 RESOLUTION RANGE LOW (A) : 44.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.000 REMARK 200 R MERGE (I) : 0.04601 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.8900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.15000 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: PHENIX REMARK 200 STARTING MODEL: 1PTY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 8K, 0.15 M MAGNESIUM ACETATE, REMARK 280 0.1 M MES (PH 6.5), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 281.15K 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 34.88300 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 69.76600 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 69.76600 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 34.88300 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 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 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 2 CG CD OE1 OE2 REMARK 470 LYS A 5 CG CD CE NZ REMARK 470 GLU A 8 CG CD OE1 OE2 REMARK 470 GLN A 9 CD OE1 NE2 REMARK 470 LYS A 12 CG CD CE NZ REMARK 470 ARG A 33 CD NE CZ NH1 NH2 REMARK 470 LYS A 41 CE NZ REMARK 470 GLU A 61 CG CD OE1 OE2 REMARK 470 GLU A 62 CG CD OE1 OE2 REMARK 470 GLU A 136 CG CD OE1 OE2 REMARK 470 GLU A 186 CG CD OE1 OE2 REMARK 470 GLU A 207 CD OE1 OE2 REMARK 470 LYS A 237 CG CD CE NZ REMARK 470 ARG A 238 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 293 CG CD OE1 OE2 REMARK 470 HIS A 296 CG ND1 CD2 CE1 NE2 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 ASP A 63 -73.80 -58.47 REMARK 500 CYS A 215 -134.18 -129.90 REMARK 500 ILE A 219 -36.84 -133.08 REMARK 500 ILE A 261 111.68 76.23 REMARK 500 REMARK 500 REMARK: NULL DBREF 8EXI A 1 297 UNP P18031 PTN1_HUMAN 1 297 SEQADV 8EXI GLU A 61 UNP P18031 GLN 61 CONFLICT SEQADV 8EXI ALA A 181 UNP P18031 ASP 181 ENGINEERED MUTATION SEQADV 8EXI ALA A 262 UNP P18031 GLN 262 ENGINEERED MUTATION SEQADV 8EXI ALA A 298 UNP P18031 EXPRESSION TAG SEQRES 1 A 298 MET GLU MET GLU LYS GLU PHE GLU GLN ILE ASP LYS SER SEQRES 2 A 298 GLY SER TRP ALA ALA ILE TYR GLN ASP ILE ARG HIS GLU SEQRES 3 A 298 ALA SER ASP PHE PRO CYS ARG VAL ALA LYS LEU PRO LYS SEQRES 4 A 298 ASN LYS ASN ARG ASN ARG TYR ARG ASP VAL SER PRO PHE SEQRES 5 A 298 ASP HIS SER ARG ILE LYS LEU HIS GLU GLU ASP ASN ASP SEQRES 6 A 298 TYR ILE ASN ALA SER LEU ILE LYS MET GLU GLU ALA GLN SEQRES 7 A 298 ARG SER TYR ILE LEU THR GLN GLY PRO LEU PRO ASN THR SEQRES 8 A 298 CYS GLY HIS PHE TRP GLU MET VAL TRP GLU GLN LYS SER SEQRES 9 A 298 ARG GLY VAL VAL MET LEU ASN ARG VAL MET GLU LYS GLY SEQRES 10 A 298 SER LEU LYS CYS ALA GLN TYR TRP PRO GLN LYS GLU GLU SEQRES 11 A 298 LYS GLU MET ILE PHE GLU ASP THR ASN LEU LYS LEU THR SEQRES 12 A 298 LEU ILE SER GLU ASP ILE LYS SER TYR TYR THR VAL ARG SEQRES 13 A 298 GLN LEU GLU LEU GLU ASN LEU THR THR GLN GLU THR ARG SEQRES 14 A 298 GLU ILE LEU HIS PHE HIS TYR THR THR TRP PRO ALA PHE SEQRES 15 A 298 GLY VAL PRO GLU SER PRO ALA SER PHE LEU ASN PHE LEU SEQRES 16 A 298 PHE LYS VAL ARG GLU SER GLY SER LEU SER PRO GLU HIS SEQRES 17 A 298 GLY PRO VAL VAL VAL HIS CYS SER ALA GLY ILE GLY ARG SEQRES 18 A 298 SER GLY THR PHE CYS LEU ALA ASP THR CYS LEU LEU LEU SEQRES 19 A 298 MET ASP LYS ARG LYS ASP PRO SER SER VAL ASP ILE LYS SEQRES 20 A 298 LYS VAL LEU LEU GLU MET ARG LYS PHE ARG MET GLY LEU SEQRES 21 A 298 ILE ALA THR ALA ASP GLN LEU ARG PHE SER TYR LEU ALA SEQRES 22 A 298 VAL ILE GLU GLY ALA LYS PHE ILE MET GLY ASP SER SER SEQRES 23 A 298 VAL GLN ASP GLN TRP LYS GLU LEU SER HIS GLU ALA HET MES A 301 25 HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID FORMUL 2 MES C6 H13 N O4 S FORMUL 3 HOH *160(H2 O) HELIX 1 AA1 MET A 1 GLY A 14 1 14 HELIX 2 AA2 SER A 15 ALA A 27 1 13 HELIX 3 AA3 LEU A 37 ASN A 44 5 8 HELIX 4 AA4 THR A 91 LYS A 103 1 13 HELIX 5 AA5 SER A 187 SER A 201 1 15 HELIX 6 AA6 GLY A 220 LYS A 239 1 20 HELIX 7 AA7 ASP A 240 VAL A 244 5 5 HELIX 8 AA8 ASP A 245 ARG A 254 1 10 HELIX 9 AA9 THR A 263 MET A 282 1 20 HELIX 10 AB1 SER A 286 SER A 295 1 10 SHEET 1 AA1 9 ARG A 56 LYS A 58 0 SHEET 2 AA1 9 TYR A 66 MET A 74 -1 O ALA A 69 N ILE A 57 SHEET 3 AA1 9 ARG A 79 THR A 84 -1 O TYR A 81 N ILE A 72 SHEET 4 AA1 9 VAL A 211 HIS A 214 1 O VAL A 213 N ILE A 82 SHEET 5 AA1 9 GLY A 106 MET A 109 1 N VAL A 108 O VAL A 212 SHEET 6 AA1 9 THR A 168 TYR A 176 1 O PHE A 174 N VAL A 107 SHEET 7 AA1 9 TYR A 153 ASN A 162 -1 N LEU A 158 O ILE A 171 SHEET 8 AA1 9 LEU A 140 ILE A 149 -1 N ASP A 148 O VAL A 155 SHEET 9 AA1 9 MET A 133 PHE A 135 -1 N PHE A 135 O LEU A 140 SHEET 1 AA2 2 MET A 114 GLU A 115 0 SHEET 2 AA2 2 SER A 118 LEU A 119 -1 O SER A 118 N GLU A 115 CRYST1 88.719 88.719 104.649 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 0.011272 0.006508 0.000000 0.00000 SCALE2 0.000000 0.013015 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009556 0.00000