HEADER HYDROLASE, SIGNALING PROTEIN 11-OCT-00 1G1F TITLE CRYSTAL STRUCTURE OF PROTEIN TYROSINE PHOSPHATASE 1B COMPLEXED WITH A TITLE 2 TRI-PHOSPHORYLATED PEPTIDE (RDI(PTR)ETD(PTR)(PTR)RK) FROM THE INSULIN TITLE 3 RECEPTOR KINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN TYROSINE PHOSPHATASE 1B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: PTP1B, PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1; COMPND 6 EC: 3.1.3.48; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: TRI-PHOSPHORYLATED PEPTIDE FROM THE INSULIN RECEPTOR COMPND 11 KINASE; COMPND 12 CHAIN: B; COMPND 13 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; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-19B; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 OTHER_DETAILS: SEQUENCE FROM THE ACTIVATION SEGMENT OF THE INSULIN SOURCE 12 RECPTOR KINASE KEYWDS HYDROLASE (PHOSPHORYLATION), TYROSINE PHOSPHATASE, PEPTIDE COMPLEX, KEYWDS 2 HYDROLASE, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.SALMEEN,J.N.ANDERSEN,M.P.MYERS,N.K.TONKS,D.BARFORD REVDAT 6 30-OCT-24 1G1F 1 REMARK REVDAT 5 03-NOV-21 1G1F 1 SEQADV LINK REVDAT 4 24-FEB-09 1G1F 1 VERSN REVDAT 3 01-APR-03 1G1F 1 JRNL REVDAT 2 17-SEP-01 1G1F 1 AUTHOR JRNL REVDAT 1 17-JAN-01 1G1F 0 JRNL AUTH A.SALMEEN,J.N.ANDERSEN,M.P.MYERS,N.K.TONKS,D.BARFORD JRNL TITL MOLECULAR BASIS FOR THE DEPHOSPHORYLATION OF THE ACTIVATION JRNL TITL 2 SEGMENT OF THE INSULIN RECEPTOR BY PROTEIN TYROSINE JRNL TITL 3 PHOSPHATASE 1B. JRNL REF MOL.CELL V. 6 1401 2000 JRNL REFN ISSN 1097-2765 JRNL PMID 11163213 JRNL DOI 10.1016/S1097-2765(00)00137-4 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : CNS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 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) (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 22388 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) : 0.207 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1136 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 : 2485 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 247 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.03 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) : 0.022 REMARK 3 BOND ANGLES (DEGREES) : 3.300 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 1G1F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-OCT-00. REMARK 100 THE DEPOSITION ID IS D_1000012113. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-99 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8700 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24096 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 75.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.71 REMARK 200 R MERGE FOR SHELL (I) : 0.20000 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: NULL 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 (%): 49.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, MGCL2, DITHIOTHREITOL, REMARK 280 HEPES, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 302.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 44.56200 REMARK 290 SMTRY3 2 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A MONOMER CONSTRUCTED FROM CHAIN REMARK 300 A 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 ARG B 1155 REMARK 465 ASP B 1156 REMARK 465 ILE B 1157 REMARK 465 PTR B 1158 REMARK 465 LYS B 1165 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 62 CG CD OE1 OE2 REMARK 470 LYS A 116 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 LYS A 131 75.45 -115.57 REMARK 500 ALA A 215 -138.21 -140.75 REMARK 500 ILE A 219 -42.44 -130.35 REMARK 500 ILE A 261 111.48 81.83 REMARK 500 PTR B1163 29.76 -68.49 REMARK 500 REMARK 500 REMARK: NULL DBREF 1G1F A 1 298 UNP P18031 PTN1_HUMAN 1 298 DBREF 1G1F B 1155 1165 PDB 1G1F 1G1F 1155 1165 SEQADV 1G1F ALA A 215 UNP P18031 CYS 215 ENGINEERED MUTATION 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 GLN 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 ASP 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 ALA 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 GLN 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 ASP SEQRES 1 B 11 ARG ASP ILE PTR GLU THR ASP PTR PTR ARG LYS MODRES 1G1F PTR B 1162 TYR O-PHOSPHOTYROSINE MODRES 1G1F PTR B 1163 TYR O-PHOSPHOTYROSINE HET PTR B1162 16 HET PTR B1163 16 HETNAM PTR O-PHOSPHOTYROSINE HETSYN PTR PHOSPHONOTYROSINE FORMUL 2 PTR 2(C9 H12 N O6 P) FORMUL 3 HOH *247(H2 O) HELIX 1 1 GLU A 2 GLY A 14 1 13 HELIX 2 2 SER A 15 ALA A 27 1 13 HELIX 3 3 LEU A 37 ASN A 44 5 8 HELIX 4 4 THR A 91 GLN A 102 1 12 HELIX 5 5 SER A 187 SER A 201 1 15 HELIX 6 6 ILE A 219 ARG A 238 1 20 HELIX 7 7 ASP A 240 VAL A 244 5 5 HELIX 8 8 ASP A 245 ARG A 254 1 10 HELIX 9 9 THR A 263 MET A 282 1 20 HELIX 10 10 SER A 286 HIS A 296 1 11 SHEET 1 A 9 ARG A 56 LYS A 58 0 SHEET 2 A 9 TYR A 66 MET A 74 -1 N ILE A 67 O ILE A 57 SHEET 3 A 9 ARG A 79 THR A 84 -1 O ARG A 79 N MET A 74 SHEET 4 A 9 VAL A 211 HIS A 214 1 O VAL A 211 N ILE A 82 SHEET 5 A 9 GLY A 106 MET A 109 1 O GLY A 106 N VAL A 212 SHEET 6 A 9 THR A 168 TYR A 176 1 O LEU A 172 N VAL A 107 SHEET 7 A 9 TYR A 153 ASN A 162 -1 O THR A 154 N HIS A 175 SHEET 8 A 9 LEU A 140 ILE A 149 -1 O LYS A 141 N GLU A 161 SHEET 9 A 9 MET A 133 PHE A 135 -1 O MET A 133 N LEU A 142 LINK C ASP B1161 N PTR B1162 1555 1555 1.33 LINK C PTR B1162 N PTR B1163 1555 1555 1.34 LINK C PTR B1163 N ARG B1164 1555 1555 1.34 CRYST1 42.545 89.124 50.126 90.00 111.19 90.00 P 1 21 1 2 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 0.023505 0.000000 0.009112 0.00000 SCALE2 0.000000 0.011220 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021396 0.00000