PDB Short entry for 1P14 HEADER TRANSFERASE 11-APR-03 1P14 TITLE CRYSTAL STRUCTURE OF A CATALYTIC-LOOP MUTANT OF THE INSULIN RECEPTOR TITLE 2 TYROSINE KINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: INSULIN RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TYROSINE KINASE DOMAIN, RESIDUES 978-1283; COMPND 5 EC: 2.7.1.112; 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 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS RECEPTOR, TYROSINE KINASE, CATALYSIS, MUTANT, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.LI,N.D.COVINO,E.G.STEIN,J.H.TILL,S.R.HUBBARD REVDAT 4 16-AUG-23 1P14 1 REMARK REVDAT 3 27-OCT-21 1P14 1 SEQADV REVDAT 2 24-FEB-09 1P14 1 VERSN REVDAT 1 22-JUL-03 1P14 0 JRNL AUTH S.LI,N.D.COVINO,E.G.STEIN,J.H.TILL,S.R.HUBBARD JRNL TITL STRUCTURAL AND BIOCHEMICAL EVIDENCE FOR AN AUTOINHIBITORY JRNL TITL 2 ROLE FOR TYROSINE 984 IN THE JUXTAMEMBRANE REGION OF THE JRNL TITL 3 INSULIN RECEPTOR JRNL REF J.BIOL.CHEM. V. 278 26007 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12707268 JRNL DOI 10.1074/JBC.M302425200 REMARK 2 REMARK 2 RESOLUTION. 1.90 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.71 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) (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 27883 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) : 0.224 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1368 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4153 REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE : 0.2900 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 225 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2233 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 188 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.78000 REMARK 3 B22 (A**2) : 1.85000 REMARK 3 B33 (A**2) : -1.06000 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) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.14 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) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.23 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.760 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) : 0.690 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.210 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.580 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.310 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.48 REMARK 3 BSOL : 67.17 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 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1P14 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-APR-03. REMARK 100 THE DEPOSITION ID IS D_1000018884. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-APR-01 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRANDEIS - B4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29657 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.030 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.29800 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: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1I44 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.50 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 28.73600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.40700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.74100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.40700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.73600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.74100 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 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 1153 REMARK 465 THR A 1154 REMARK 465 ARG A 1155 REMARK 465 ASP A 1156 REMARK 465 ILE A 1157 REMARK 465 TYR A 1158 REMARK 465 GLU A 1159 REMARK 465 THR A 1160 REMARK 465 ASP A 1161 REMARK 465 TYR A 1162 REMARK 465 TYR A 1163 REMARK 465 ARG A 1164 REMARK 465 LYS A 1165 REMARK 465 GLY A 1166 REMARK 465 GLY A 1167 REMARK 465 LYS A 1168 REMARK 465 GLY A 1169 REMARK 465 LEU A 1170 REMARK 465 LEU A 1171 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 994 CG CD OE1 OE2 REMARK 470 GLU A1034 CG CD OE1 OE2 REMARK 470 LYS A1068 CG CD CE NZ REMARK 470 GLU A1094 CG CD OE1 OE2 REMARK 470 GLU A1096 CG CD OE1 OE2 REMARK 470 ARG A1101 CG CD NE CZ NH1 NH2 REMARK 470 ARG A1136 CG CD NE CZ NH1 NH2 REMARK 470 GLN A1211 CG CD OE1 NE2 REMARK 470 LYS A1220 CG CD CE NZ REMARK 470 ARG A1243 CG CD NE CZ NH1 NH2 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 PRO A 986 88.02 -62.14 REMARK 500 ASP A 987 -142.37 -113.73 REMARK 500 PRO A1099 4.54 -68.54 REMARK 500 ARG A1131 -11.95 74.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IRK RELATED DB: PDB DBREF 1P14 A 978 1283 UNP P06213 INSR_HUMAN 993 1298 SEQADV 1P14 SER A 981 UNP P06213 CYS 996 ENGINEERED MUTATION SEQADV 1P14 ASN A 1132 UNP P06213 ASP 1147 ENGINEERED MUTATION SEQRES 1 A 306 VAL PHE PRO SER SER VAL TYR VAL PRO ASP GLU TRP GLU SEQRES 2 A 306 VAL SER ARG GLU LYS ILE THR LEU LEU ARG GLU LEU GLY SEQRES 3 A 306 GLN GLY SER PHE GLY MET VAL TYR GLU GLY ASN ALA ARG SEQRES 4 A 306 ASP ILE ILE LYS GLY GLU ALA GLU THR ARG VAL ALA VAL SEQRES 5 A 306 LYS THR VAL ASN GLU SER ALA SER LEU ARG GLU ARG ILE SEQRES 6 A 306 GLU PHE LEU ASN GLU ALA SER VAL MET LYS GLY PHE THR SEQRES 7 A 306 CYS HIS HIS VAL VAL ARG LEU LEU GLY VAL VAL SER LYS SEQRES 8 A 306 GLY GLN PRO THR LEU VAL VAL MET GLU LEU MET ALA HIS SEQRES 9 A 306 GLY ASP LEU LYS SER TYR LEU ARG SER LEU ARG PRO GLU SEQRES 10 A 306 ALA GLU ASN ASN PRO GLY ARG PRO PRO PRO THR LEU GLN SEQRES 11 A 306 GLU MET ILE GLN MET ALA ALA GLU ILE ALA ASP GLY MET SEQRES 12 A 306 ALA TYR LEU ASN ALA LYS LYS PHE VAL HIS ARG ASN LEU SEQRES 13 A 306 ALA ALA ARG ASN CYS MET VAL ALA HIS ASP PHE THR VAL SEQRES 14 A 306 LYS ILE GLY ASP PHE GLY MET THR ARG ASP ILE TYR GLU SEQRES 15 A 306 THR ASP TYR TYR ARG LYS GLY GLY LYS GLY LEU LEU PRO SEQRES 16 A 306 VAL ARG TRP MET ALA PRO GLU SER LEU LYS ASP GLY VAL SEQRES 17 A 306 PHE THR THR SER SER ASP MET TRP SER PHE GLY VAL VAL SEQRES 18 A 306 LEU TRP GLU ILE THR SER LEU ALA GLU GLN PRO TYR GLN SEQRES 19 A 306 GLY LEU SER ASN GLU GLN VAL LEU LYS PHE VAL MET ASP SEQRES 20 A 306 GLY GLY TYR LEU ASP GLN PRO ASP ASN CYS PRO GLU ARG SEQRES 21 A 306 VAL THR ASP LEU MET ARG MET CYS TRP GLN PHE ASN PRO SEQRES 22 A 306 ASN MET ARG PRO THR PHE LEU GLU ILE VAL ASN LEU LEU SEQRES 23 A 306 LYS ASP ASP LEU HIS PRO SER PHE PRO GLU VAL SER PHE SEQRES 24 A 306 PHE HIS SER GLU GLU ASN LYS FORMUL 2 HOH *188(H2 O) HELIX 1 1 SER A 992 GLU A 994 5 3 HELIX 2 2 SER A 1037 LYS A 1052 1 16 HELIX 3 3 ASP A 1083 LEU A 1091 1 9 HELIX 4 4 THR A 1105 LYS A 1126 1 22 HELIX 5 5 ALA A 1134 ARG A 1136 5 3 HELIX 6 6 PRO A 1172 MET A 1176 5 5 HELIX 7 7 ALA A 1177 GLY A 1184 1 8 HELIX 8 8 THR A 1187 SER A 1204 1 18 HELIX 9 9 SER A 1214 ASP A 1224 1 11 HELIX 10 10 PRO A 1235 TRP A 1246 1 12 HELIX 11 11 ASN A 1249 ARG A 1253 5 5 HELIX 12 12 THR A 1255 LYS A 1264 1 10 HELIX 13 13 ASP A 1265 LEU A 1267 5 3 HELIX 14 14 SER A 1270 SER A 1275 1 6 SHEET 1 A 5 ILE A 996 GLN A1004 0 SHEET 2 A 5 MET A1009 ILE A1019 -1 O GLU A1012 N ARG A1000 SHEET 3 A 5 GLU A1022 LYS A1030 -1 O VAL A1029 N TYR A1011 SHEET 4 A 5 LEU A1073 GLU A1077 -1 O MET A1076 N ALA A1028 SHEET 5 A 5 LEU A1062 VAL A1066 -1 N VAL A1066 O LEU A1073 SHEET 1 B 2 CYS A1138 VAL A1140 0 SHEET 2 B 2 VAL A1146 ILE A1148 -1 O LYS A1147 N MET A1139 CISPEP 1 GLN A 1070 PRO A 1071 0 -0.11 CRYST1 57.472 69.482 88.814 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 0.017400 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014392 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011259 0.00000