HEADER ONCOPROTEIN 14-JUN-18 6A32 TITLE CRYSTAL STRUCTURE OF PDGFRA KINASE DOMAIN MUTANT T674I COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLATELET-DERIVED GROWTH FACTOR RECEPTOR ALPHA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PDGFR-ALPHA,ALPHA PLATELET-DERIVED GROWTH FACTOR RECEPTOR, COMPND 5 ALPHA-TYPE PLATELET-DERIVED GROWTH FACTOR RECEPTOR,CD140 ANTIGEN-LIKE COMPND 6 FAMILY MEMBER A,CD140A ANTIGEN,PLATELET-DERIVED GROWTH FACTOR ALPHA COMPND 7 RECEPTOR,PLATELET-DERIVED GROWTH FACTOR RECEPTOR 2,PDGFR-2; COMPND 8 EC: 2.7.10.1; COMPND 9 ENGINEERED: YES; COMPND 10 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: PDGFRA, PDGFR2, RHEPDGFRA; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS PDGFRA, T674I, RECEPTOR TYROSINE KINASE, ONCOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.E.YAN,L.LIANG,C.H.YUN REVDAT 2 22-NOV-23 6A32 1 REMARK REVDAT 1 19-JUN-19 6A32 0 JRNL AUTH X.E.YAN,L.LIANG,C.H.YUN JRNL TITL CRYSTAL STRUCTURE OF PDGFRA KINASE DOMAIN MUTANT T674I JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 26260 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.770 REMARK 3 FREE R VALUE TEST SET COUNT : 1252 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 34.7035 - 3.8888 1.00 3039 137 0.2013 0.2126 REMARK 3 2 3.8888 - 3.0873 1.00 2860 141 0.1999 0.2234 REMARK 3 3 3.0873 - 2.6972 1.00 2838 156 0.1991 0.2208 REMARK 3 4 2.6972 - 2.4507 1.00 2813 137 0.2079 0.2678 REMARK 3 5 2.4507 - 2.2751 1.00 2821 146 0.2016 0.2517 REMARK 3 6 2.2751 - 2.1409 1.00 2788 136 0.2015 0.2572 REMARK 3 7 2.1409 - 2.0337 1.00 2784 145 0.2028 0.2770 REMARK 3 8 2.0337 - 1.9452 0.98 2701 133 0.2139 0.2530 REMARK 3 9 1.9452 - 1.8703 0.85 2364 121 0.2377 0.3333 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.340 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 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 : 0.011 2770 REMARK 3 ANGLE : 1.167 3743 REMARK 3 CHIRALITY : 0.098 404 REMARK 3 PLANARITY : 0.009 468 REMARK 3 DIHEDRAL : 22.752 1030 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 6A32 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1300008081. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9777 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26260 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.870 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 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: PHASER REMARK 200 STARTING MODEL: 5K5X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PH 5.5, 27% PEG 3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 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 18.59700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.16600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.80200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.16600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.59700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.80200 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 GLY A 546 REMARK 465 ALA A 547 REMARK 465 MET A 548 REMARK 465 ASP A 549 REMARK 465 LYS A 550 REMARK 465 GLN A 551 REMARK 465 LYS A 552 REMARK 465 PRO A 553 REMARK 465 SER A 776 REMARK 465 GLU A 777 REMARK 465 VAL A 778 REMARK 465 LYS A 779 REMARK 465 ASN A 780 REMARK 465 LEU A 781 REMARK 465 LEU A 782 REMARK 465 SER A 783 REMARK 465 ASP A 784 REMARK 465 ASP A 785 REMARK 465 ASN A 786 REMARK 465 SER A 787 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 584 35.33 -99.88 REMARK 500 ASP A 818 38.66 -146.52 REMARK 500 REMARK 500 REMARK: NULL DBREF 6A32 A 550 696 UNP P16234 PGFRA_HUMAN 550 696 DBREF 6A32 A 769 973 UNP P16234 PGFRA_HUMAN 769 973 SEQADV 6A32 GLY A 546 UNP P16234 EXPRESSION TAG SEQADV 6A32 ALA A 547 UNP P16234 EXPRESSION TAG SEQADV 6A32 MET A 548 UNP P16234 EXPRESSION TAG SEQADV 6A32 ASP A 549 UNP P16234 EXPRESSION TAG SEQADV 6A32 ILE A 674 UNP P16234 THR 674 ENGINEERED MUTATION SEQRES 1 A 356 GLY ALA MET ASP LYS GLN LYS PRO ARG TYR GLU ILE ARG SEQRES 2 A 356 TRP ARG VAL ILE GLU SER ILE SER PRO ASP GLY HIS GLU SEQRES 3 A 356 TYR ILE TYR VAL ASP PRO MET GLN LEU PRO TYR ASP SER SEQRES 4 A 356 ARG TRP GLU PHE PRO ARG ASP GLY LEU VAL LEU GLY ARG SEQRES 5 A 356 VAL LEU GLY SER GLY ALA PHE GLY LYS VAL VAL GLU GLY SEQRES 6 A 356 THR ALA TYR GLY LEU SER ARG SER GLN PRO VAL MET LYS SEQRES 7 A 356 VAL ALA VAL LYS MET LEU LYS PRO THR ALA ARG SER SER SEQRES 8 A 356 GLU LYS GLN ALA LEU MET SER GLU LEU LYS ILE MET THR SEQRES 9 A 356 HIS LEU GLY PRO HIS LEU ASN ILE VAL ASN LEU LEU GLY SEQRES 10 A 356 ALA CYS THR LYS SER GLY PRO ILE TYR ILE ILE ILE GLU SEQRES 11 A 356 TYR CYS PHE TYR GLY ASP LEU VAL ASN TYR LEU HIS LYS SEQRES 12 A 356 ASN ARG ASP SER PHE LEU SER HIS LYS LYS LYS SER MET SEQRES 13 A 356 LEU ASP SER GLU VAL LYS ASN LEU LEU SER ASP ASP ASN SEQRES 14 A 356 SER GLU GLY LEU THR LEU LEU ASP LEU LEU SER PHE THR SEQRES 15 A 356 TYR GLN VAL ALA ARG GLY MET GLU PHE LEU ALA SER LYS SEQRES 16 A 356 ASN CYS VAL HIS ARG ASP LEU ALA ALA ARG ASN VAL LEU SEQRES 17 A 356 LEU ALA GLN GLY LYS ILE VAL LYS ILE CYS ASP PHE GLY SEQRES 18 A 356 LEU ALA ARG ASP ILE MET HIS ASP SER ASN TYR VAL SER SEQRES 19 A 356 LYS GLY SER THR PHE LEU PRO VAL LYS TRP MET ALA PRO SEQRES 20 A 356 GLU SER ILE PHE ASP ASN LEU TYR THR THR LEU SER ASP SEQRES 21 A 356 VAL TRP SER TYR GLY ILE LEU LEU TRP GLU ILE PHE SER SEQRES 22 A 356 LEU GLY GLY THR PRO TYR PRO GLY MET MET VAL ASP SER SEQRES 23 A 356 THR PHE TYR ASN LYS ILE LYS SER GLY TYR ARG MET ALA SEQRES 24 A 356 LYS PRO ASP HIS ALA THR SER GLU VAL TYR GLU ILE MET SEQRES 25 A 356 VAL LYS CYS TRP ASN SER GLU PRO GLU LYS ARG PRO SER SEQRES 26 A 356 PHE TYR HIS LEU SER GLU ILE VAL GLU ASN LEU LEU PRO SEQRES 27 A 356 GLY GLN TYR LYS LYS SER TYR GLU LYS ILE HIS LEU ASP SEQRES 28 A 356 PHE LEU LYS SER ASP FORMUL 2 HOH *93(H2 O) HELIX 1 AA1 ASP A 576 LEU A 580 5 5 HELIX 2 AA2 PRO A 589 ASP A 591 5 3 HELIX 3 AA3 ARG A 634 GLY A 652 1 19 HELIX 4 AA4 LEU A 682 ASN A 689 1 8 HELIX 5 AA5 ASN A 689 ASP A 775 1 15 HELIX 6 AA6 THR A 791 LYS A 812 1 22 HELIX 7 AA7 ALA A 820 ARG A 822 5 3 HELIX 8 AA8 PHE A 837 ARG A 841 5 5 HELIX 9 AA9 ASP A 842 ASP A 846 5 5 HELIX 10 AB1 PRO A 858 MET A 862 5 5 HELIX 11 AB2 ALA A 863 ASN A 870 1 8 HELIX 12 AB3 THR A 873 SER A 890 1 18 HELIX 13 AB4 ASP A 902 GLY A 912 1 11 HELIX 14 AB5 THR A 922 TRP A 933 1 12 HELIX 15 AB6 GLU A 936 ARG A 940 5 5 HELIX 16 AB7 SER A 942 ASN A 952 1 11 HELIX 17 AB8 PRO A 955 SER A 972 1 18 SHEET 1 AA1 3 TYR A 572 TYR A 574 0 SHEET 2 AA1 3 ARG A 560 ILE A 565 -1 N GLU A 563 O ILE A 573 SHEET 3 AA1 3 CYS A 814 VAL A 815 -1 O VAL A 815 N ARG A 560 SHEET 1 AA2 5 LEU A 593 SER A 601 0 SHEET 2 AA2 5 GLY A 605 TYR A 613 -1 O GLU A 609 N GLY A 596 SHEET 3 AA2 5 VAL A 621 LEU A 629 -1 O MET A 622 N ALA A 612 SHEET 4 AA2 5 TYR A 671 GLU A 675 -1 O ILE A 674 N ALA A 625 SHEET 5 AA2 5 LEU A 660 CYS A 664 -1 N LEU A 661 O ILE A 673 SHEET 1 AA3 3 GLY A 680 ASP A 681 0 SHEET 2 AA3 3 VAL A 824 ALA A 827 -1 O LEU A 826 N GLY A 680 SHEET 3 AA3 3 ILE A 831 ILE A 834 -1 O ILE A 831 N ALA A 827 SHEET 1 AA4 2 VAL A 850 LYS A 852 0 SHEET 2 AA4 2 THR A 855 LEU A 857 -1 O LEU A 857 N VAL A 850 CRYST1 37.194 87.604 96.332 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 0.026886 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011415 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010381 0.00000