HEADER TRANSFERASE 01-AUG-22 8DWN TITLE CRYSTAL STRUCTURE OF BIS-PHOSPHORYLATED INSULIN RECEPTOR KINASE DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: INSULIN RECEPTOR SUBUNIT BETA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: INSR; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS INSULIN RECEPTOR, TYROSINE KINASE, PHOSPHORYLATION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.R.HUBBARD REVDAT 2 15-NOV-23 8DWN 1 REMARK REVDAT 1 16-AUG-23 8DWN 0 JRNL AUTH S.R.HUBBARD JRNL TITL CRYSTAL STRUCTURE OF BIS-PHOSPHORYLATED INSULIN RECEPTOR JRNL TITL 2 KINASE DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.0 REMARK 3 NUMBER OF REFLECTIONS : 18050 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1805 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 32.6400 - 5.0500 0.81 1218 136 0.1872 0.2248 REMARK 3 2 5.0500 - 4.0100 0.86 1246 138 0.1604 0.2086 REMARK 3 3 4.0100 - 3.5100 0.87 1228 136 0.1693 0.2160 REMARK 3 4 3.5000 - 3.1800 0.88 1238 138 0.1938 0.2338 REMARK 3 5 3.1800 - 2.9600 0.88 1241 138 0.2089 0.2571 REMARK 3 6 2.9600 - 2.7800 0.90 1253 139 0.1984 0.2858 REMARK 3 7 2.7800 - 2.6400 0.90 1252 139 0.2134 0.2756 REMARK 3 8 2.6400 - 2.5300 0.91 1253 139 0.2042 0.2841 REMARK 3 9 2.5300 - 2.4300 0.91 1278 142 0.1973 0.2789 REMARK 3 10 2.4300 - 2.3500 0.92 1258 141 0.2024 0.2706 REMARK 3 11 2.3500 - 2.2700 0.92 1278 140 0.2130 0.3022 REMARK 3 12 2.2700 - 2.2100 0.92 1267 141 0.1954 0.2789 REMARK 3 13 2.2100 - 2.1500 0.90 1235 138 0.1954 0.2786 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.236 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.376 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.93 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 2296 REMARK 3 ANGLE : 0.969 3107 REMARK 3 CHIRALITY : 0.058 339 REMARK 3 PLANARITY : 0.012 402 REMARK 3 DIHEDRAL : 8.264 309 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8DWN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1000267440. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-OCT-97 REMARK 200 TEMPERATURE (KELVIN) : 110 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18050 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 32.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.9 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : 0.04830 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.7800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.14800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.830 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: 1IRK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 6000, 0.2 M MALATE-IMIDAZOLE, REMARK 280 PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K 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 28.97150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.38750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.09450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.38750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.97150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.09450 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 VAL A 978 REMARK 465 PHE A 979 REMARK 465 PRO A 980 REMARK 465 SER A 981 REMARK 465 SER A 982 REMARK 465 VAL A 983 REMARK 465 PHE A 984 REMARK 465 VAL A 985 REMARK 465 PRO A 986 REMARK 465 PHE A 1151 REMARK 465 GLY A 1152 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 PTR A 1158 REMARK 465 GLU A 1159 REMARK 465 THR A 1160 REMARK 465 ASP A 1161 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 ASP A 987 CG OD1 OD2 REMARK 470 GLU A 988 CG CD OE1 OE2 REMARK 470 GLU A1094 CG CD OE1 OE2 REMARK 470 GLU A1096 CG CD OE1 OE2 REMARK 470 ASP A1150 CG OD1 OD2 REMARK 470 ARG A1164 CG CD NE CZ NH1 NH2 REMARK 470 LYS A1165 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 ARG A1131 -19.69 86.56 REMARK 500 ASP A1132 37.75 -140.38 REMARK 500 ALA A1134 153.85 179.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1519 DISTANCE = 5.95 ANGSTROMS DBREF 8DWN A 978 1283 UNP P06213 INSR_HUMAN 1005 1310 SEQADV 8DWN SER A 981 UNP P06213 CYS 1008 ENGINEERED MUTATION SEQADV 8DWN PHE A 984 UNP P06213 TYR 1011 ENGINEERED MUTATION SEQRES 1 A 306 VAL PHE PRO SER SER VAL PHE 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 ASP 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 PTR GLU SEQRES 15 A 306 THR ASP PTR 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 LYS 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 MODRES 8DWN PTR A 1162 TYR MODIFIED RESIDUE HET PTR A1162 16 HETNAM PTR O-PHOSPHOTYROSINE HETSYN PTR PHOSPHONOTYROSINE FORMUL 1 PTR C9 H12 N O6 P FORMUL 2 HOH *219(H2 O) HELIX 1 AA1 SER A 992 GLU A 994 5 3 HELIX 2 AA2 SER A 1037 LYS A 1052 1 16 HELIX 3 AA3 ASP A 1083 SER A 1090 1 8 HELIX 4 AA4 THR A 1105 LYS A 1126 1 22 HELIX 5 AA5 ALA A 1134 ARG A 1136 5 3 HELIX 6 AA6 PRO A 1172 MET A 1176 5 5 HELIX 7 AA7 ALA A 1177 GLY A 1184 1 8 HELIX 8 AA8 THR A 1187 SER A 1204 1 18 HELIX 9 AA9 SER A 1214 ASP A 1224 1 11 HELIX 10 AB1 PRO A 1235 TRP A 1246 1 12 HELIX 11 AB2 ASN A 1249 ARG A 1253 5 5 HELIX 12 AB3 THR A 1255 LYS A 1264 1 10 HELIX 13 AB4 ASP A 1265 LEU A 1267 5 3 HELIX 14 AB5 SER A 1270 SER A 1275 1 6 HELIX 15 AB6 SER A 1279 LYS A 1283 5 5 SHEET 1 AA1 5 ILE A 996 GLN A1004 0 SHEET 2 AA1 5 MET A1009 ILE A1019 -1 O VAL A1010 N LEU A1002 SHEET 3 AA1 5 GLU A1022 LYS A1030 -1 O VAL A1029 N TYR A1011 SHEET 4 AA1 5 LEU A1073 GLU A1077 -1 O VAL A1074 N LYS A1030 SHEET 5 AA1 5 LEU A1062 VAL A1066 -1 N VAL A1066 O LEU A1073 SHEET 1 AA2 2 CYS A1138 VAL A1140 0 SHEET 2 AA2 2 VAL A1146 ILE A1148 -1 O LYS A1147 N MET A1139 LINK C PTR A1162 N TYR A1163 1555 1555 1.33 CISPEP 1 GLN A 1070 PRO A 1071 0 0.16 CRYST1 57.943 70.189 88.775 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 0.017258 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014247 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011264 0.00000