PDB Short entry for 1L8K HEADER HYDROLASE 21-MAR-02 1L8K TITLE T CELL PROTEIN-TYROSINE PHOSPHATASE STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: T-CELL PROTEIN-TYROSINE PHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 2, TCPTP; COMPND 5 EC: 3.1.3.48; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN TYROSINE PHOSPHATASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.F.IVERSEN REVDAT 4 14-FEB-24 1L8K 1 REMARK REVDAT 3 24-FEB-09 1L8K 1 VERSN REVDAT 2 28-AUG-02 1L8K 1 JRNL REVDAT 1 08-MAY-02 1L8K 0 JRNL AUTH L.F.IVERSEN,K.B.MOLLER,A.K.PEDERSEN,G.H.PETERS,A.S.PETERSEN, JRNL AUTH 2 H.S.ANDERSEN,S.BRANNER,S.B.MORTENSEN,N.P.MOLLER JRNL TITL STRUCTURE DETERMINATION OF T CELL PROTEIN-TYROSINE JRNL TITL 2 PHOSPHATASE. JRNL REF J.BIOL.CHEM. V. 277 19982 2002 JRNL REFN ISSN 0021-9258 JRNL PMID 11907034 JRNL DOI 10.1074/JBC.M200567200 REMARK 2 REMARK 2 RESOLUTION. 2.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 11665 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 583 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2244 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 40 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1L8K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAR-02. REMARK 100 THE DEPOSITION ID IS D_1000015740. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11665 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.560 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, HEPES, MGSO4, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 93.81650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.24700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.24700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 140.72475 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.24700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.24700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 46.90825 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.24700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.24700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 140.72475 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.24700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.24700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 46.90825 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 93.81650 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 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 MET A 1 REMARK 465 PRO A 2 REMARK 465 THR A 3 REMARK 465 THR A 4 REMARK 465 CYS A 278 REMARK 465 ILE A 279 REMARK 465 LYS A 280 REMARK 465 GLY A 281 REMARK 465 ASP A 282 REMARK 465 SER A 283 REMARK 465 SER A 284 REMARK 465 ILE A 285 REMARK 465 GLN A 286 REMARK 465 LYS A 287 REMARK 465 ARG A 288 REMARK 465 TRP A 289 REMARK 465 LYS A 290 REMARK 465 GLU A 291 REMARK 465 LEU A 292 REMARK 465 SER A 293 REMARK 465 LYS A 294 REMARK 465 GLU A 295 REMARK 465 ASP A 296 REMARK 465 LEU A 297 REMARK 465 SER A 298 REMARK 465 PRO A 299 REMARK 465 ALA A 300 REMARK 465 PHE A 301 REMARK 465 ASP A 302 REMARK 465 HIS A 303 REMARK 465 SER A 304 REMARK 465 PRO A 305 REMARK 465 ASN A 306 REMARK 465 LYS A 307 REMARK 465 ILE A 308 REMARK 465 MET A 309 REMARK 465 THR A 310 REMARK 465 GLU A 311 REMARK 465 LYS A 312 REMARK 465 TYR A 313 REMARK 465 ASN A 314 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 GLN A 15 9.42 -62.04 REMARK 500 GLU A 78 -8.65 -55.02 REMARK 500 LYS A 118 -44.91 -29.93 REMARK 500 GLU A 119 5.37 56.10 REMARK 500 LYS A 122 -87.42 -49.64 REMARK 500 CYS A 123 80.91 41.63 REMARK 500 SER A 166 -6.99 -155.95 REMARK 500 PHE A 183 123.87 66.36 REMARK 500 PRO A 207 3.76 -63.45 REMARK 500 CYS A 216 -149.67 -126.51 REMARK 500 ILE A 220 -31.20 -137.74 REMARK 500 GLU A 237 -15.19 67.00 REMARK 500 LYS A 238 -102.98 -126.10 REMARK 500 ASP A 240 -170.27 -170.59 REMARK 500 ILE A 259 102.10 72.17 REMARK 500 ALA A 276 28.92 -67.92 REMARK 500 REMARK 500 REMARK: NULL DBREF 1L8K A 1 314 UNP P17706 PTN2_HUMAN 1 314 SEQRES 1 A 314 MET PRO THR THR ILE GLU ARG GLU PHE GLU GLU LEU ASP SEQRES 2 A 314 THR GLN ARG ARG TRP GLN PRO LEU TYR LEU GLU ILE ARG SEQRES 3 A 314 ASN GLU SER HIS ASP TYR PRO HIS ARG VAL ALA LYS PHE SEQRES 4 A 314 PRO GLU ASN ARG ASN ARG ASN ARG TYR ARG ASP VAL SER SEQRES 5 A 314 PRO TYR ASP HIS SER ARG VAL LYS LEU GLN ASN ALA GLU SEQRES 6 A 314 ASN ASP TYR ILE ASN ALA SER LEU VAL ASP ILE GLU GLU SEQRES 7 A 314 ALA GLN ARG SER TYR ILE LEU THR GLN GLY PRO LEU PRO SEQRES 8 A 314 ASN THR CYS CYS HIS PHE TRP LEU MET VAL TRP GLN GLN SEQRES 9 A 314 LYS THR LYS ALA VAL VAL MET LEU ASN ARG ILE VAL GLU SEQRES 10 A 314 LYS GLU SER VAL LYS CYS ALA GLN TYR TRP PRO THR ASP SEQRES 11 A 314 ASP GLN GLU MET LEU PHE LYS GLU THR GLY PHE SER VAL SEQRES 12 A 314 LYS LEU LEU SER GLU ASP VAL LYS SER TYR TYR THR VAL SEQRES 13 A 314 HIS LEU LEU GLN LEU GLU ASN ILE ASN SER GLY GLU THR SEQRES 14 A 314 ARG THR ILE SER HIS PHE HIS TYR THR THR TRP PRO ASP SEQRES 15 A 314 PHE GLY VAL PRO GLU SER PRO ALA SER PHE LEU ASN PHE SEQRES 16 A 314 LEU PHE LYS VAL ARG GLU SER GLY SER LEU ASN PRO ASP SEQRES 17 A 314 HIS GLY PRO ALA VAL ILE HIS CYS SER ALA GLY ILE GLY SEQRES 18 A 314 ARG SER GLY THR PHE SER LEU VAL ASP THR CYS LEU VAL SEQRES 19 A 314 LEU MET GLU LYS GLY ASP ASP ILE ASN ILE LYS GLN VAL SEQRES 20 A 314 LEU LEU ASN MET ARG LYS TYR ARG MET GLY LEU ILE GLN SEQRES 21 A 314 THR PRO ASP GLN LEU ARG PHE SER TYR MET ALA ILE ILE SEQRES 22 A 314 GLU GLY ALA LYS CYS ILE LYS GLY ASP SER SER ILE GLN SEQRES 23 A 314 LYS ARG TRP LYS GLU LEU SER LYS GLU ASP LEU SER PRO SEQRES 24 A 314 ALA PHE ASP HIS SER PRO ASN LYS ILE MET THR GLU LYS SEQRES 25 A 314 TYR ASN FORMUL 2 HOH *40(H2 O) HELIX 1 1 GLU A 6 GLN A 15 1 10 HELIX 2 2 TRP A 18 SER A 29 1 12 HELIX 3 3 HIS A 34 PHE A 39 1 6 HELIX 4 4 PRO A 40 ASN A 46 5 7 HELIX 5 5 GLU A 77 GLN A 80 5 4 HELIX 6 6 THR A 93 GLN A 104 1 12 HELIX 7 7 PRO A 189 SER A 202 1 14 HELIX 8 8 GLY A 221 MET A 236 1 16 HELIX 9 9 ASN A 243 ARG A 252 1 10 HELIX 10 10 THR A 261 ALA A 276 1 16 SHEET 1 A 9 ARG A 58 LYS A 60 0 SHEET 2 A 9 TYR A 68 ILE A 76 -1 N ILE A 69 O VAL A 59 SHEET 3 A 9 ARG A 81 GLN A 87 -1 O ARG A 81 N ILE A 76 SHEET 4 A 9 ALA A 212 CYS A 216 1 O ALA A 212 N ILE A 84 SHEET 5 A 9 ALA A 108 MET A 111 1 O ALA A 108 N VAL A 213 SHEET 6 A 9 THR A 169 TYR A 177 1 O SER A 173 N VAL A 109 SHEET 7 A 9 TYR A 154 ASN A 163 -1 O THR A 155 N HIS A 176 SHEET 8 A 9 PHE A 141 VAL A 150 -1 O SER A 142 N GLU A 162 SHEET 9 A 9 MET A 134 PHE A 136 -1 O MET A 134 N VAL A 143 CRYST1 60.494 60.494 187.633 90.00 90.00 90.00 P 43 21 2 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 0.016531 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016531 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005330 0.00000