HEADER HYDROLASE 01-JUN-16 5KA4 TITLE PROTEIN TYROSINE PHOSPHATASE 1B T178A MUTANT, OPEN STATE 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: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) KEYWDS PROTEIN TYROSINE PHOSPHATASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.S.CHOY,W.PETI,R.PAGE REVDAT 2 28-FEB-24 5KA4 1 REMARK REVDAT 1 08-MAR-17 5KA4 0 JRNL AUTH M.S.CHOY,Y.LI,L.E.MACHADO,M.B.KUNZE,C.R.CONNORS,X.WEI, JRNL AUTH 2 K.LINDORFF-LARSEN,R.PAGE,W.PETI JRNL TITL CONFORMATIONAL RIGIDITY AND PROTEIN DYNAMICS AT DISTINCT JRNL TITL 2 TIMESCALES REGULATE PTP1B ACTIVITY AND ALLOSTERY. JRNL REF MOL. CELL V. 65 644 2017 JRNL REFN ISSN 1097-4164 JRNL PMID 28212750 JRNL DOI 10.1016/J.MOLCEL.2017.01.014 REMARK 2 REMARK 2 RESOLUTION. 2.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 3 NUMBER OF REFLECTIONS : 15406 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850 REMARK 3 FREE R VALUE TEST SET COUNT : 747 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 35.0989 - 3.7357 0.87 2870 152 0.1774 0.2036 REMARK 3 2 3.7357 - 2.9656 0.93 3030 133 0.1984 0.2192 REMARK 3 3 2.9656 - 2.5909 0.94 2984 187 0.2304 0.2821 REMARK 3 4 2.5909 - 2.3541 0.93 2995 122 0.2403 0.3091 REMARK 3 5 2.3541 - 2.1854 0.87 2780 153 0.2663 0.3118 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.000 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.28 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.39 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 : 0.002 2267 REMARK 3 ANGLE : 0.440 3072 REMARK 3 CHIRALITY : 0.040 336 REMARK 3 PLANARITY : 0.003 398 REMARK 3 DIHEDRAL : 12.050 1362 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 5KA4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000221948. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.9 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15410 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.170 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.12400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.49800 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 2.5.6 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS, PH 8.0, 0.2 M MGCL2, 17% REMARK 280 PEG8000, 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 58.60250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.25050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.60250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.25050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 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 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 GLY A -4 REMARK 465 HIS A -3 REMARK 465 MET A -2 REMARK 465 ALA A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 MET A 282 REMARK 465 GLY A 283 REMARK 465 ASP A 284 REMARK 465 SER A 285 REMARK 465 SER A 286 REMARK 465 VAL A 287 REMARK 465 GLN A 288 REMARK 465 ASP A 289 REMARK 465 GLN A 290 REMARK 465 TRP A 291 REMARK 465 LYS A 292 REMARK 465 GLU A 293 REMARK 465 LEU A 294 REMARK 465 SER A 295 REMARK 465 HIS A 296 REMARK 465 GLU A 297 REMARK 465 ASP A 298 REMARK 465 LEU A 299 REMARK 465 GLU A 300 REMARK 465 PRO A 301 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 5 CG CD CE NZ REMARK 470 LYS A 12 CG CD CE NZ REMARK 470 GLU A 26 CG CD OE1 OE2 REMARK 470 LYS A 41 CG CD CE NZ REMARK 470 GLU A 62 CG CD OE1 OE2 REMARK 470 ASP A 63 CG OD1 OD2 REMARK 470 GLU A 97 CG CD OE1 OE2 REMARK 470 LYS A 116 CG CD CE NZ REMARK 470 LYS A 120 CG CD CE NZ REMARK 470 LYS A 128 CG CD CE NZ REMARK 470 GLU A 130 CG CD OE1 OE2 REMARK 470 LYS A 131 CG CD CE NZ REMARK 470 GLU A 136 CG CD OE1 OE2 REMARK 470 GLN A 166 CG CD OE1 NE2 REMARK 470 GLU A 186 CG CD OE1 OE2 REMARK 470 LYS A 239 CG CD CE NZ REMARK 470 LYS A 247 CG CD CE NZ REMARK 470 LYS A 279 CG CD CE NZ 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 CYS A 215 -133.23 -122.79 REMARK 500 ILE A 219 -34.60 -135.38 REMARK 500 ILE A 261 106.10 66.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5K9V RELATED DB: PDB REMARK 900 RELATED ID: 5KA7 RELATED DB: PDB REMARK 900 RELATED ID: 5KA8 RELATED DB: PDB REMARK 900 RELATED ID: 5KA9 RELATED DB: PDB REMARK 900 RELATED ID: 5KAA RELATED DB: PDB REMARK 900 RELATED ID: 5KAB RELATED DB: PDB REMARK 900 RELATED ID: 5KAC RELATED DB: PDB REMARK 900 RELATED ID: 5KAD RELATED DB: PDB REMARK 900 RELATED ID: 5K9W RELATED DB: PDB REMARK 900 RELATED ID: 5KA0 RELATED DB: PDB REMARK 900 RELATED ID: 5KA1 RELATED DB: PDB REMARK 900 RELATED ID: 5KA2 RELATED DB: PDB REMARK 900 RELATED ID: 5KA3 RELATED DB: PDB DBREF 5KA4 A 1 301 UNP P18031 PTN1_HUMAN 1 301 SEQADV 5KA4 GLY A -4 UNP P18031 EXPRESSION TAG SEQADV 5KA4 HIS A -3 UNP P18031 EXPRESSION TAG SEQADV 5KA4 MET A -2 UNP P18031 EXPRESSION TAG SEQADV 5KA4 ALA A -1 UNP P18031 EXPRESSION TAG SEQADV 5KA4 SER A 0 UNP P18031 EXPRESSION TAG SEQADV 5KA4 ALA A 178 UNP P18031 THR 178 ENGINEERED MUTATION SEQRES 1 A 306 GLY HIS MET ALA SER MET GLU MET GLU LYS GLU PHE GLU SEQRES 2 A 306 GLN ILE ASP LYS SER GLY SER TRP ALA ALA ILE TYR GLN SEQRES 3 A 306 ASP ILE ARG HIS GLU ALA SER ASP PHE PRO CYS ARG VAL SEQRES 4 A 306 ALA LYS LEU PRO LYS ASN LYS ASN ARG ASN ARG TYR ARG SEQRES 5 A 306 ASP VAL SER PRO PHE ASP HIS SER ARG ILE LYS LEU HIS SEQRES 6 A 306 GLN GLU ASP ASN ASP TYR ILE ASN ALA SER LEU ILE LYS SEQRES 7 A 306 MET GLU GLU ALA GLN ARG SER TYR ILE LEU THR GLN GLY SEQRES 8 A 306 PRO LEU PRO ASN THR CYS GLY HIS PHE TRP GLU MET VAL SEQRES 9 A 306 TRP GLU GLN LYS SER ARG GLY VAL VAL MET LEU ASN ARG SEQRES 10 A 306 VAL MET GLU LYS GLY SER LEU LYS CYS ALA GLN TYR TRP SEQRES 11 A 306 PRO GLN LYS GLU GLU LYS GLU MET ILE PHE GLU ASP THR SEQRES 12 A 306 ASN LEU LYS LEU THR LEU ILE SER GLU ASP ILE LYS SER SEQRES 13 A 306 TYR TYR THR VAL ARG GLN LEU GLU LEU GLU ASN LEU THR SEQRES 14 A 306 THR GLN GLU THR ARG GLU ILE LEU HIS PHE HIS TYR THR SEQRES 15 A 306 ALA TRP PRO ASP PHE GLY VAL PRO GLU SER PRO ALA SER SEQRES 16 A 306 PHE LEU ASN PHE LEU PHE LYS VAL ARG GLU SER GLY SER SEQRES 17 A 306 LEU SER PRO GLU HIS GLY PRO VAL VAL VAL HIS CYS SER SEQRES 18 A 306 ALA GLY ILE GLY ARG SER GLY THR PHE CYS LEU ALA ASP SEQRES 19 A 306 THR CYS LEU LEU LEU MET ASP LYS ARG LYS ASP PRO SER SEQRES 20 A 306 SER VAL ASP ILE LYS LYS VAL LEU LEU GLU MET ARG LYS SEQRES 21 A 306 PHE ARG MET GLY LEU ILE GLN THR ALA ASP GLN LEU ARG SEQRES 22 A 306 PHE SER TYR LEU ALA VAL ILE GLU GLY ALA LYS PHE ILE SEQRES 23 A 306 MET GLY ASP SER SER VAL GLN ASP GLN TRP LYS GLU LEU SEQRES 24 A 306 SER HIS GLU ASP LEU GLU PRO FORMUL 2 HOH *80(H2 O) HELIX 1 AA1 GLU A 2 GLY A 14 1 13 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 GLN A 102 1 12 HELIX 5 AA5 PRO A 188 SER A 201 1 14 HELIX 6 AA6 GLY A 220 ARG A 238 1 19 HELIX 7 AA7 ASP A 240 VAL A 244 5 5 HELIX 8 AA8 ASP A 245 LYS A 255 1 11 HELIX 9 AA9 THR A 263 ILE A 281 1 19 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 GLU A 167 TYR A 176 1 O PHE A 174 N VAL A 107 SHEET 7 AA1 9 TYR A 153 ASN A 162 -1 N THR A 154 O HIS A 175 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 MET A 133 O LEU A 142 CRYST1 117.205 46.501 59.911 90.00 90.39 90.00 C 1 2 1 4 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 0.008532 0.000000 0.000058 0.00000 SCALE2 0.000000 0.021505 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016692 0.00000