HEADER HYDROLASE 16-JUL-01 1JLN TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PROTEIN TYROSINE TITLE 2 PHOSPHATASE PTP-SL/BR7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN TYROSINE PHOSPHATASE, RECEPTOR TYPE, R; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: STEP-LIKE PTPASE; PROTEIN-TYROSINE-PHOSPHATASE RECEPTOR TYPE COMPND 6 PTPBR7; PTPBR7; COMPND 7 EC: 3.1.3.48; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: DH5ALPHA; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-2T KEYWDS PROTEIN TYROSINE PHOSPHATASE, PTP-SL, PTPBR7, ERK2-MAP KINASE KEYWDS 2 REGULATION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.E.SZEDLACSEK,A.R.ARICESCU,T.A.FULGA,L.RENAULT,A.J.SCHEIDIG REVDAT 3 16-AUG-23 1JLN 1 REMARK SEQADV REVDAT 2 24-FEB-09 1JLN 1 VERSN REVDAT 1 17-AUG-01 1JLN 0 JRNL AUTH S.E.SZEDLACSEK,A.R.ARICESCU,T.A.FULGA,L.RENAULT,A.J.SCHEIDIG JRNL TITL CRYSTAL STRUCTURE OF PTP-SL/PTPBR7 CATALYTIC DOMAIN: JRNL TITL 2 IMPLICATIONS FOR MAP KINASE REGULATION. JRNL REF J.MOL.BIOL. V. 311 557 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11493009 JRNL DOI 10.1006/JMBI.2001.4890 REMARK 2 REMARK 2 RESOLUTION. 1.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 197719.790 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 83.7 REMARK 3 NUMBER OF REFLECTIONS : 24970 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1248 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 44.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2108 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE : 0.2960 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 111 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.028 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2364 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 238 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.09000 REMARK 3 B22 (A**2) : 0.21000 REMARK 3 B33 (A**2) : 2.88000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.12 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.840 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 3.460 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.310 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.120 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.430 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 43.44 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1JLN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUL-01. REMARK 100 THE DEPOSITION ID IS D_1000013913. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JAN-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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 : SIEMENS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS HI-STAR REMARK 200 INTENSITY-INTEGRATION SOFTWARE : X-GEN REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24970 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.810 REMARK 200 RESOLUTION RANGE LOW (A) : 19.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.7 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : 5.70000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 40.3 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 : 2.620 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: 1YFO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, PH 7.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP AT 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 23.06800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.83500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.66100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.83500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.06800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.66100 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 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 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 SER A 281 64.64 -107.32 REMARK 500 SER A 282 48.24 -70.88 REMARK 500 GLU A 301 -83.98 -60.90 REMARK 500 LYS A 329 27.02 -75.65 REMARK 500 ASN A 330 30.99 -169.54 REMARK 500 SER A 334 -54.56 64.93 REMARK 500 ILE A 383 58.22 -119.03 REMARK 500 LYS A 389 -50.06 85.98 REMARK 500 LYS A 400 -41.14 -144.53 REMARK 500 CYS A 417 -159.66 -151.45 REMARK 500 ASP A 418 -96.15 -44.42 REMARK 500 CYS A 480 -122.93 -135.54 REMARK 500 SER A 481 -64.48 -95.73 REMARK 500 ILE A 484 -35.26 -136.18 REMARK 500 VAL A 523 85.99 63.14 REMARK 500 REMARK 500 REMARK: NULL DBREF 1JLN A 254 548 UNP Q62132 PTPRR_MOUSE 254 548 SEQADV 1JLN GLY A 252 UNP Q62132 CLONING ARTIFACT SEQADV 1JLN SER A 253 UNP Q62132 CLONING ARTIFACT SEQRES 1 A 297 GLY SER PRO ARG GLU LYS VAL ALA MET GLU TYR LEU GLN SEQRES 2 A 297 SER ALA SER ARG VAL LEU THR ARG SER GLN LEU ARG ASP SEQRES 3 A 297 VAL VAL ALA SER SER HIS LEU LEU GLN SER GLU PHE MET SEQRES 4 A 297 GLU ILE PRO MET ASN PHE VAL ASP PRO LYS GLU ILE ASP SEQRES 5 A 297 ILE PRO ARG HIS GLY THR LYS ASN ARG TYR LYS THR ILE SEQRES 6 A 297 LEU PRO ASN PRO LEU SER ARG VAL CYS LEU ARG PRO LYS SEQRES 7 A 297 ASN ILE THR ASP SER LEU SER THR TYR ILE ASN ALA ASN SEQRES 8 A 297 TYR ILE ARG GLY TYR SER GLY LYS GLU LYS ALA PHE ILE SEQRES 9 A 297 ALA THR GLN GLY PRO MET ILE ASN THR VAL ASN ASP PHE SEQRES 10 A 297 TRP GLN MET VAL TRP GLN GLU ASP SER PRO VAL ILE VAL SEQRES 11 A 297 MET ILE THR LYS LEU LYS GLU LYS ASN GLU LYS CYS VAL SEQRES 12 A 297 LEU TYR TRP PRO GLU LYS ARG GLY ILE TYR GLY LYS VAL SEQRES 13 A 297 GLU VAL LEU VAL THR GLY VAL THR GLU CYS ASP ASN TYR SEQRES 14 A 297 THR ILE ARG ASN LEU VAL LEU LYS GLN GLY SER HIS THR SEQRES 15 A 297 GLN HIS VAL LYS HIS TYR TRP TYR THR SER TRP PRO ASP SEQRES 16 A 297 HIS LYS THR PRO ASP SER ALA GLN PRO LEU LEU GLN LEU SEQRES 17 A 297 MET LEU ASP VAL GLU GLU ASP ARG LEU ALA SER GLU GLY SEQRES 18 A 297 ARG GLY PRO VAL VAL VAL HIS CYS SER ALA GLY ILE GLY SEQRES 19 A 297 ARG THR GLY CYS PHE ILE ALA THR SER ILE GLY CYS GLN SEQRES 20 A 297 GLN LEU LYS GLU GLU GLY VAL VAL ASP ALA LEU SER ILE SEQRES 21 A 297 VAL CYS GLN LEU ARG VAL ASP ARG GLY GLY MET VAL GLN SEQRES 22 A 297 THR SER GLU GLN TYR GLU PHE VAL HIS HIS ALA LEU CYS SEQRES 23 A 297 LEU PHE GLU SER ARG LEU SER PRO GLU THR VAL FORMUL 2 HOH *238(H2 O) HELIX 1 1 ARG A 255 ALA A 266 1 12 HELIX 2 2 ARG A 272 SER A 281 1 10 HELIX 3 3 HIS A 283 ILE A 292 1 10 HELIX 4 4 ARG A 306 ASN A 311 5 6 HELIX 5 5 ASN A 319 SER A 322 5 4 HELIX 6 6 SER A 334 TYR A 338 5 5 HELIX 7 7 GLY A 346 LYS A 350 5 5 HELIX 8 8 MET A 361 ASN A 363 5 3 HELIX 9 9 THR A 364 GLU A 375 1 12 HELIX 10 10 ALA A 453 ALA A 469 1 17 HELIX 11 11 ILE A 484 GLY A 504 1 21 HELIX 12 12 ASP A 507 ARG A 519 1 13 HELIX 13 13 THR A 525 ARG A 542 1 18 SHEET 1 A 2 LEU A 270 THR A 271 0 SHEET 2 A 2 VAL A 505 VAL A 506 -1 O VAL A 506 N LEU A 270 SHEET 1 B 8 ALA A 341 ILE A 344 0 SHEET 2 B 8 PHE A 354 THR A 357 -1 O PHE A 354 N ILE A 344 SHEET 3 B 8 VAL A 476 HIS A 479 1 O VAL A 476 N ILE A 355 SHEET 4 B 8 VAL A 379 MET A 382 1 O VAL A 379 N VAL A 477 SHEET 5 B 8 HIS A 432 TYR A 441 1 O LYS A 437 N ILE A 380 SHEET 6 B 8 TYR A 420 GLN A 429 -1 O THR A 421 N TRP A 440 SHEET 7 B 8 VAL A 407 GLU A 416 -1 N GLU A 408 O LYS A 428 SHEET 8 B 8 ARG A 401 TYR A 404 -1 O GLY A 402 N VAL A 409 CRYST1 46.136 65.322 105.670 90.00 90.00 90.00 P 21 21 21 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 0.021675 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015309 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009463 0.00000