HEADER HYDROLASE 16-SEP-94 1YPT 1YPT 2 COMPND PROTEIN-TYROSINE PHOSPHATASE (YERSINIA) (E.C.3.1.3.48) 1YPT 3 COMPND 2 (YOP51,PASTEURELLA X,PTPASE,YOP51DELTA162) (CATALYTIC 1YPT 4 COMPND 3 DOMAIN, RESIDUES 163 - 468) MUTANT WITH CYS 235 1YPT 5 COMPND 4 REPLACED BY ARG (C235R) 1YPT 6 SOURCE YERSINIA (YERSINIA ENTEROCOLITICA, STRAIN W22703) 1YPT 7 SOURCE 2 RECOMBINANT FORM EXPRESSED IN (ESCHERICHIA COLI, BL21(DE3)) 1YPT 8 SOURCE 3 PLASMID: PT7-7, GENE: YOP51 1YPT 9 AUTHOR J.A.STUCKEY,H.L.SCHUBERT,E.B.FAUMAN,Z.-Y.ZHANG,J.E.DIXON, 1YPT 10 AUTHOR 2 M.A.SAPER 1YPT 11 REVDAT 1 20-DEC-94 1YPT 0 1YPT 12 JRNL AUTH J.A.STUCKEY,H.L.SCHUBERT,E.B.FAUMAN,Z.-Y.ZHANG, 1YPT 13 JRNL AUTH 2 J.E.DIXON,M.A.SAPER 1YPT 14 JRNL TITL CRYSTAL STRUCTURE OF YERSINIA PROTEIN TYROSINE 1YPT 15 JRNL TITL 2 PHOSPHATASE AT 2.5 ANGSTROMS AND THE COMPLEX WITH 1YPT 16 JRNL TITL 3 TUNGSTATE 1YPT 17 JRNL REF NATURE V. 370 571 1994 1YPT 18 JRNL REFN ASTM NATUAS UK ISSN 0028-0836 0006 1YPT 19 REMARK 1 1YPT 20 REMARK 1 REFERENCE 1 1YPT 21 REMARK 1 AUTH Z.-Y.ZHANG,J.C.CLEMENS,H.L.SCHUBERT,J.A.STUCKEY, 1YPT 22 REMARK 1 AUTH 2 M.W.F.FISCHER,D.M.HUME,M.A.SAPER,J.E.DIXON 1YPT 23 REMARK 1 TITL EXPRESSION, PURIFICATION, AND PHYSICOCHEMICAL 1YPT 24 REMARK 1 TITL 2 CHARACTERIZATION OF A RECOMBINANT YERSINIA 1YPT 25 REMARK 1 TITL 3 PROTEIN TYROSINE PHOSPHATASE 1YPT 26 REMARK 1 REF J.BIOL.CHEM. V. 267 23759 1992 1YPT 27 REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258 0071 1YPT 28 REMARK 2 1YPT 29 REMARK 2 RESOLUTION. 2.5 ANGSTROMS. 1YPT 30 REMARK 3 1YPT 31 REMARK 3 REFINEMENT. 1YPT 32 REMARK 3 PROGRAM X-PLOR 1YPT 33 REMARK 3 AUTHORS BRUNGER 1YPT 34 REMARK 3 R VALUE 0.168 1YPT 35 REMARK 3 FREE R VALUE 0.222 1YPT 36 REMARK 3 NUMBER OF REFLECTIONS 17095 1YPT 37 REMARK 3 RESOLUTION RANGE 7.0 - 2.5 ANGSTROMS 1YPT 38 REMARK 3 DATA CUTOFF 2. SIGMA(F) 1YPT 39 REMARK 3 COMPLETENESS FOR RANGE 84.0 % 1YPT 40 REMARK 3 1YPT 41 REMARK 3 DATA COLLECTION. 1YPT 42 REMARK 3 NUMBER OF UNIQUE REFLECTIONS 19476 1YPT 43 REMARK 3 COMPLETENESS OF DATA 91.0 % 1YPT 44 REMARK 3 REJECTION CRITERIA 0. SIGMA(I) 1YPT 45 REMARK 3 1YPT 46 REMARK 3 SOLVENT CONTENT (VS) 48.9 % 1YPT 47 REMARK 3 1YPT 48 REMARK 3 NUMBER OF ATOMS USED IN REFINEMENT. 1YPT 49 REMARK 3 NUMBER OF PROTEIN ATOMS 4292 1YPT 50 REMARK 3 NUMBER OF NUCLEIC ACID ATOMS 0 1YPT 51 REMARK 3 NUMBER OF SOLVENT ATOMS 64 1YPT 52 REMARK 3 1YPT 53 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES (THE VALUES OF 1YPT 54 REMARK 3 SIGMA, IN PARENTHESES, ARE THE INPUT ESTIMATED 1YPT 55 REMARK 3 STANDARD DEVIATIONS THAT DETERMINE THE RELATIVE 1YPT 56 REMARK 3 WEIGHTS OF THE CORRESPONDING RESTRAINTS). 1YPT 57 REMARK 3 DISTANCE RESTRAINTS (ANGSTROMS). 1YPT 58 REMARK 3 BOND DISTANCE 0.013 1YPT 59 REMARK 3 ANGLE RESTRAINTS (DEGREES). 1YPT 60 REMARK 3 BOND ANGLES 2.93 1YPT 61 REMARK 3 DIHEDRAL ANGLES 24.81 1YPT 62 REMARK 3 IMPROPER TORSION ANGLES 1.25 1YPT 63 REMARK 4 1YPT 64 REMARK 4 THE ELECTRON DENSITY IS CONTIGUOUS, WHEN CONTOURED AT 1 1YPT 65 REMARK 4 STANDARD DEVIATION, FOR ALL MAIN CHAIN ATOMS WITH THE 1YPT 66 REMARK 4 EXCEPTION OF THE FOLLOWING ATOMS: N GLU A 224, 1YPT 67 REMARK 4 CA ASP A 356, C GLN A357, N THR A 358, N GLY B 222, 1YPT 68 REMARK 4 CA GLY B 222, AND CA GLY B 223. 1YPT 69 REMARK 5 1YPT 70 REMARK 5 COMPND 1YPT 71 REMARK 6 THE CATALYTIC DOMAIN (RESIDUES 163 - 468) OF YOP51 WAS 1YPT 72 REMARK 6 CRYSTALLIZED AT 22 DEGREES CELSIUS, IN A SOLUTION OF 1YPT 73 REMARK 6 10 - 16% POLYETHYLENE GLYCOL, 5% 2-METHYL-2,4-PENTANEDIOL, 1YPT 74 REMARK 6 0.1% B-MERCAPTOETHANOL, AND 1MM IMIDAZOLE, PH 7.2. 1YPT 75 REMARK 6 1YPT 76 REMARK 6 SOURCE 1YPT 77 REMARK 6 ONLY THE CATALYTIC DOMAIN (RESIDUES 163 - 468) WAS 1YPT 78 REMARK 6 EXPRESSED FOR THIS PARTICULAR EXPERIMENT. THE 235 CYS TO 1YPT 79 REMARK 6 ARG MUTATION WAS UNINTENTIONAL AND MOST LIKELY THE 1YPT 80 REMARK 6 RESULT OF USING PCR TO CONSTRUCT THE PLASMID (SEE 1YPT 81 REMARK 6 REFERENCE REMARK 1). 1YPT 82 REMARK 7 1YPT 83 REMARK 7 CROSS REFERENCE TO SEQUENCE DATABASE 1YPT 84 REMARK 7 DATABASE: SWISS-PROT 1YPT 85 REMARK 7 ENTRY_NAME: P15273 1YPT 86 REMARK 8 1YPT 87 REMARK 8 SITE 1YPT 88 REMARK 8 SITE_IDENTIFIER: APL 1YPT 89 REMARK 8 THE PHOSPHATE BINDING LOOP WHICH IS BELIEVED TO BE 1YPT 90 REMARK 8 STRUCTURALLY CONSERVED IN ALL PROTEIN TYROSINE 1YPT 91 REMARK 8 PHOSPHATASES. 1YPT 92 REMARK 8 SITE_IDENTIFIER: BPL 1YPT 93 REMARK 8 THE PHOSPHATE BINDING LOOP WHICH IS BELIEVED TO BE 1YPT 94 REMARK 8 STRUCTURALLY CONSERVED IN ALL PROTEIN TYROSINE 1YPT 95 REMARK 8 PHOSPHATASES. 1YPT 96 REMARK 8 SITE_IDENTIFIER: WPD 1YPT 97 REMARK 8 THE FLEXIBLE LOOP FROM MOLECULE B CONTAINING THE 1YPT 98 REMARK 8 PUTATIVE GENERAL ACID, ASP 356, THAT FOLDS OVER THE 1YPT 99 REMARK 8 ACTIVE SITE AND SEQUESTERS THE TUNGSTATE ANION IN THE 1YPT 100 REMARK 8 TUNGSTATE-BOUND STRUCTURE. 1YPT 101 REMARK 9 1YPT 102 REMARK 9 MTRIX 1YPT 103 REMARK 9 THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW 1YPT 104 REMARK 9 DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE 1YPT 105 REMARK 9 VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE 1YPT 106 REMARK 9 MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL 1YPT 107 REMARK 9 YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED 1YPT 108 REMARK 9 SECOND. 1YPT 109 REMARK 9 1YPT 110 REMARK 9 APPLIED TO TRANSFORMED TO 1YPT 111 REMARK 9 MTRIX CHAIN RESIDUES CHAIN RESIDUES RMSD 1YPT 112 REMARK 9 M1 A 191 - A 468 B 191 - B 468 .223 1YPT 113 REMARK 9 1YPT 114 REMARK 9 A 178.02 DEGREE ROTATION ABOUT THE X AXIS OF THE CRYSTAL 1YPT 115 REMARK 9 THAT RELATES MOLECULE A TO MOLECULE B. THE RMSD 1YPT 116 REMARK 9 (EXCLUDING 4 FLEXIBLE LOOPS) BETWEEN MOLECULE A AND 1YPT 117 REMARK 9 MOLECULE B IS 0.196. THE RMSD USING ALL ATOMS IS 0.523. 1YPT 118 REMARK 10 1YPT 119 REMARK 10 KEYWDS: PROTEIN TYROSINE PHOSPHATASE 1YPT 120 REMARK 11 1YPT 121 REMARK 11 CROSS REFERENCE TO SEQUENCE DATABASE 1YPT 122 REMARK 11 SWISS-PROT ENTRY NAME PDB ENTRY CHAIN NAME 1YPT 123 REMARK 11 YOPH_YEREN A 1YPT 124 REMARK 11 YOPH_YEREN B 1YPT 125 REMARK 11 1YPT 126 REMARK 11 SEQUENCE ADVISORY NOTICE 1YPT 127 REMARK 11 DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. 1YPT 128 REMARK 11 1YPT 129 REMARK 11 SWISS-PROT RESIDUE PDB SEQRES 1YPT 130 REMARK 11 1YPT 131 REMARK 11 NAME NUMBER NAME CHAIN SEQ/INSERT CODE 1YPT 132 REMARK 11 CYS 235 ARG A 235 1YPT 133 REMARK 11 CYS 235 ARG B 235 1YPT 134 REMARK 11 1YPT 135 REMARK 11 N-TERMINAL RESIDUES 163 - 190 OF CHAIN A AND 163 - 189 OF 1YPT 136 REMARK 11 CHAIN B WERE DISORDERED AND NOT VISIBLE IN THE ELECTRON 1YPT 137 REMARK 11 DENSITY MAP. 1YPT 138 SEQRES 1 A 305 ARG GLU ARG PRO HIS THR SER GLY HIS HIS GLY ALA GLY 1YPT 139 SEQRES 2 A 305 GLU ALA ARG ALA THR ALA PRO SER THR VAL SER PRO TYR 1YPT 140 SEQRES 3 A 305 GLY PRO GLU ALA ARG ALA GLU LEU SER SER ARG LEU THR 1YPT 141 SEQRES 4 A 305 THR LEU ARG ASN THR LEU ALA PRO ALA THR ASN ASP PRO 1YPT 142 SEQRES 5 A 305 ARG TYR LEU GLN ALA CYS GLY GLY GLU LYS LEU ASN ARG 1YPT 143 SEQRES 6 A 305 PHE ARG ASP ILE GLN CYS ARG ARG GLN THR ALA VAL ARG 1YPT 144 SEQRES 7 A 305 ALA ASP LEU ASN ALA ASN TYR ILE GLN VAL GLY ASN THR 1YPT 145 SEQRES 8 A 305 ARG THR ILE ALA CYS GLN TYR PRO LEU GLN SER GLN LEU 1YPT 146 SEQRES 9 A 305 GLU SER HIS PHE ARG MET LEU ALA GLU ASN ARG THR PRO 1YPT 147 SEQRES 10 A 305 VAL LEU ALA VAL LEU ALA SER SER SER GLU ILE ALA ASN 1YPT 148 SEQRES 11 A 305 GLN ARG PHE GLY MET PRO ASP TYR PHE ARG GLN SER GLY 1YPT 149 SEQRES 12 A 305 THR TYR GLY SER ILE THR VAL GLU SER LYS MET THR GLN 1YPT 150 SEQRES 13 A 305 GLN VAL GLY LEU GLY ASP GLY ILE MET ALA ASP MET TYR 1YPT 151 SEQRES 14 A 305 THR LEU THR ILE ARG GLU ALA GLY GLN LYS THR ILE SER 1YPT 152 SEQRES 15 A 305 VAL PRO VAL VAL HIS VAL GLY ASN TRP PRO ASP GLN THR 1YPT 153 SEQRES 16 A 305 ALA VAL SER SER GLU VAL THR LYS ALA LEU ALA SER LEU 1YPT 154 SEQRES 17 A 305 VAL ASP GLN THR ALA GLU THR LYS ARG ASN MET TYR GLU 1YPT 155 SEQRES 18 A 305 SER LYS GLY SER SER ALA VAL ALA ASP ASP SER LYS LEU 1YPT 156 SEQRES 19 A 305 ARG PRO VAL ILE HIS CYS ARG ALA GLY VAL GLY ARG THR 1YPT 157 SEQRES 20 A 305 ALA GLN LEU ILE GLY ALA MET CYS MET ASN ASP SER ARG 1YPT 158 SEQRES 21 A 305 ASN SER GLN LEU SER VAL GLU ASP MET VAL SER GLN MET 1YPT 159 SEQRES 22 A 305 ARG VAL GLN ARG ASN GLY ILE MET VAL GLN LYS ASP GLU 1YPT 160 SEQRES 23 A 305 GLN LEU ASP VAL LEU ILE LYS LEU ALA GLU GLY GLN GLY 1YPT 161 SEQRES 24 A 305 ARG PRO LEU LEU ASN SER 1YPT 162 SEQRES 1 B 305 ARG GLU ARG PRO HIS THR SER GLY HIS HIS GLY ALA GLY 1YPT 163 SEQRES 2 B 305 GLU ALA ARG ALA THR ALA PRO SER THR VAL SER PRO TYR 1YPT 164 SEQRES 3 B 305 GLY PRO GLU ALA ARG ALA GLU LEU SER SER ARG LEU THR 1YPT 165 SEQRES 4 B 305 THR LEU ARG ASN THR LEU ALA PRO ALA THR ASN ASP PRO 1YPT 166 SEQRES 5 B 305 ARG TYR LEU GLN ALA CYS GLY GLY GLU LYS LEU ASN ARG 1YPT 167 SEQRES 6 B 305 PHE ARG ASP ILE GLN CYS ARG ARG GLN THR ALA VAL ARG 1YPT 168 SEQRES 7 B 305 ALA ASP LEU ASN ALA ASN TYR ILE GLN VAL GLY ASN THR 1YPT 169 SEQRES 8 B 305 ARG THR ILE ALA CYS GLN TYR PRO LEU GLN SER GLN LEU 1YPT 170 SEQRES 9 B 305 GLU SER HIS PHE ARG MET LEU ALA GLU ASN ARG THR PRO 1YPT 171 SEQRES 10 B 305 VAL LEU ALA VAL LEU ALA SER SER SER GLU ILE ALA ASN 1YPT 172 SEQRES 11 B 305 GLN ARG PHE GLY MET PRO ASP TYR PHE ARG GLN SER GLY 1YPT 173 SEQRES 12 B 305 THR TYR GLY SER ILE THR VAL GLU SER LYS MET THR GLN 1YPT 174 SEQRES 13 B 305 GLN VAL GLY LEU GLY ASP GLY ILE MET ALA ASP MET TYR 1YPT 175 SEQRES 14 B 305 THR LEU THR ILE ARG GLU ALA GLY GLN LYS THR ILE SER 1YPT 176 SEQRES 15 B 305 VAL PRO VAL VAL HIS VAL GLY ASN TRP PRO ASP GLN THR 1YPT 177 SEQRES 16 B 305 ALA VAL SER SER GLU VAL THR LYS ALA LEU ALA SER LEU 1YPT 178 SEQRES 17 B 305 VAL ASP GLN THR ALA GLU THR LYS ARG ASN MET TYR GLU 1YPT 179 SEQRES 18 B 305 SER LYS GLY SER SER ALA VAL ALA ASP ASP SER LYS LEU 1YPT 180 SEQRES 19 B 305 ARG PRO VAL ILE HIS CYS ARG ALA GLY VAL GLY ARG THR 1YPT 181 SEQRES 20 B 305 ALA GLN LEU ILE GLY ALA MET CYS MET ASN ASP SER ARG 1YPT 182 SEQRES 21 B 305 ASN SER GLN LEU SER VAL GLU ASP MET VAL SER GLN MET 1YPT 183 SEQRES 22 B 305 ARG VAL GLN ARG ASN GLY ILE MET VAL GLN LYS ASP GLU 1YPT 184 SEQRES 23 B 305 GLN LEU ASP VAL LEU ILE LYS LEU ALA GLU GLY GLN GLY 1YPT 185 SEQRES 24 B 305 ARG PRO LEU LEU ASN SER 1YPT 186 FORMUL 3 HOH *65(H2 O1) 1YPT 187 HELIX 1 1 GLU A 192 LEU A 208 1 1YPT 188 HELIX 2 2 GLN A 264 GLU A 276 5 1YPT 189 HELIX 3 3 SER A 288 ALA A 292 1 1YPT 190 HELIX 4 4 GLN A 294 PHE A 296 5 1YPT 191 HELIX 5 5 SER A 362 SER A 385 1 1YPT 192 HELIX 6 6 SER A 389 ALA A 392 5 1YPT 193 HELIX 7 7 ARG A 409 ASN A 420 1 1YPT 194 HELIX 8 8 SER A 422 ASN A 424 5 1YPT 195 HELIX 9 9 VAL A 429 GLN A 439 1 1YPT 196 HELIX 10 10 ASP A 448 GLN A 461 1 1YPT 197 HELIX 11 11 PRO B 191 THR B 207 1 1YPT 198 HELIX 12 12 GLN B 264 GLU B 276 5 1YPT 199 HELIX 13 13 SER B 288 ALA B 292 1 1YPT 200 HELIX 14 14 GLN B 294 PHE B 296 5 1YPT 201 HELIX 15 15 SER B 362 LYS B 386 1 1YPT 202 HELIX 16 16 SER B 389 ALA B 392 5 1YPT 203 HELIX 17 17 ARG B 409 MET B 419 1 1YPT 204 HELIX 18 18 SER B 422 ASN B 424 5 1YPT 205 HELIX 19 19 VAL B 429 GLN B 439 1 1YPT 206 HELIX 20 20 ASP B 448 GLN B 461 1 1YPT 207 SHEET 1 A 8 ALA A 246 VAL A 251 0 1YPT 208 SHEET 2 A 8 THR A 254 CYS A 259 -1 N ALA A 258 O ASN A 247 1YPT 209 SHEET 3 A 8 PRO A 399 HIS A 402 1 N PRO A 399 O ILE A 257 1YPT 210 SHEET 4 A 8 LEU A 282 VAL A 284 1 N ALA A 283 O VAL A 400 1YPT 211 SHEET 5 A 8 ILE A 344 VAL A 351 1 N VAL A 349 O LEU A 282 1YPT 212 SHEET 6 A 8 MET A 328 GLU A 338 -1 N ILE A 336 O ILE A 344 1YPT 213 SHEET 7 A 8 ILE A 311 GLY A 322 -1 N VAL A 321 O ALA A 329 1YPT 214 SHEET 8 A 8 GLY A 306 TYR A 308 -1 N TYR A 308 O ILE A 311 1YPT 215 SHEET 1 B 8 ALA B 246 VAL B 251 0 1YPT 216 SHEET 2 B 8 THR B 254 CYS B 259 -1 N ALA B 258 O ASN B 247 1YPT 217 SHEET 3 B 8 PRO B 399 HIS B 402 1 N PRO B 399 O ILE B 257 1YPT 218 SHEET 4 B 8 LEU B 282 VAL B 284 1 N ALA B 283 O VAL B 400 1YPT 219 SHEET 5 B 8 ILE B 344 VAL B 351 1 N VAL B 349 O LEU B 282 1YPT 220 SHEET 6 B 8 MET B 328 GLU B 338 -1 N ILE B 336 O ILE B 344 1YPT 221 SHEET 7 B 8 ILE B 311 GLY B 322 -1 N VAL B 321 O ALA B 329 1YPT 222 SHEET 8 B 8 GLY B 306 TYR B 308 -1 N TYR B 308 O ILE B 311 1YPT 223 SITE 1 APL 9 HIS A 402 CYS A 403 ARG A 404 ALA A 405 1YPT 224 SITE 2 APL 9 GLY A 406 VAL A 407 GLY A 408 ARG A 409 1YPT 225 SITE 3 APL 9 THR A 410 1YPT 226 SITE 1 BPL 9 HIS B 402 CYS B 403 ARG B 404 ALA B 405 1YPT 227 SITE 2 BPL 9 GLY B 406 VAL B 407 GLY B 408 ARG B 409 1YPT 228 SITE 3 BPL 9 THR B 410 1YPT 229 SITE 1 WPD 11 HIS B 350 VAL B 351 GLY B 352 ASN B 353 1YPT 230 SITE 2 WPD 11 TRP B 354 PRO B 355 ASP B 356 GLN B 357 1YPT 231 SITE 3 WPD 11 THR B 358 ALA B 359 VAL B 360 1YPT 232 CRYST1 71.530 71.530 107.480 90.00 90.00 120.00 P 32 6 1YPT 233 ORIGX1 1.000000 0.000000 0.000000 0.00000 1YPT 234 ORIGX2 0.000000 1.000000 0.000000 0.00000 1YPT 235 ORIGX3 0.000000 0.000000 1.000000 0.00000 1YPT 236 SCALE1 0.013980 0.008071 0.000000 0.00000 1YPT 237 SCALE2 0.000000 0.016143 0.000000 0.00000 1YPT 238 SCALE3 0.000000 0.000000 0.009304 0.00000 1YPT 239 MTRIX1 1 0.992200 0.091653 0.084490 -5.65200 1 1YPT 240 MTRIX2 1 0.088672 -0.995321 0.038391 39.55800 1 1YPT 241 MTRIX3 1 0.087614 -0.030600 -0.995684 93.75700 1 1YPT 242