HEADER LIGASE 05-DEC-22 8FE0 TITLE HUMAN GAR TRANSFORMYLASE IN COMPLEX WITH GAR SUBSTRATE AND AGF305 TITLE 2 INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GART DOMAIN; COMPND 5 SYNONYM: 2-AMINO-N-RIBOSYLACETAMIDE 5'-PHOSPHATE TRANSFORMYLASE; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: GART, PGFT, PRGS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS GARFTASE, LIGASE, PURINE BIOSYNTHESIS, MONOMER EXPDTA X-RAY DIFFRACTION AUTHOR J.WONG-ROUSHAR,C.E.DANN III REVDAT 2 31-MAY-23 8FE0 1 JRNL REVDAT 1 10-MAY-23 8FE0 0 JRNL AUTH N.TONG,J.WONG-ROUSHAR,A.WALLACE-POVIRK,Y.SHAH,M.C.NYMAN, JRNL AUTH 2 J.M.KATINAS,M.SCHNEIDER,C.O'CONNOR,X.BAO,S.KIM,J.LI,Z.HOU, JRNL AUTH 3 L.H.MATHERLY,C.E.DANN 3RD,A.GANGJEE JRNL TITL MULTITARGETED 6-SUBSTITUTED THIENO[2,3- D ]PYRIMIDINES AS JRNL TITL 2 FOLATE RECEPTOR-SELECTIVE ANTICANCER AGENTS THAT INHIBIT JRNL TITL 3 CYTOSOLIC AND MITOCHONDRIAL ONE-CARBON METABOLISM. JRNL REF ACS PHARMACOL TRANSL SCI V. 6 748 2023 JRNL REFN ESSN 2575-910 JRNL PMID 37200803 JRNL DOI 10.1021/ACSPTSCI.3C00020 REMARK 2 REMARK 2 RESOLUTION. 2.22 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13-2998 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 16575 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 796 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 39.7553 - 4.0330 1.00 2770 123 0.1575 0.1774 REMARK 3 2 4.0330 - 3.2016 1.00 2647 134 0.1922 0.2470 REMARK 3 3 3.2016 - 2.7970 1.00 2627 109 0.2259 0.2706 REMARK 3 4 2.7970 - 2.5413 1.00 2601 134 0.2456 0.2866 REMARK 3 5 2.5413 - 2.3592 1.00 2572 145 0.2627 0.3214 REMARK 3 6 2.3592 - 2.2201 0.99 2562 151 0.2923 0.3635 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) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.880 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 : 0.007 1580 REMARK 3 ANGLE : 1.058 2147 REMARK 3 CHIRALITY : 0.052 256 REMARK 3 PLANARITY : 0.005 272 REMARK 3 DIHEDRAL : 16.371 942 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 8FE0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1000270410. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : RDI CMOS_8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16652 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.220 REMARK 200 RESOLUTION RANGE LOW (A) : 39.755 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.29 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: 5J9F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL PH 7.5, 0.33 M NACL, 16 REMARK 280 -21% PEG 4000, AND 2% PEG 400, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.07733 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 33.53867 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 33.53867 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 67.07733 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 807 REMARK 465 LYS A 1008 REMARK 465 GLU A 1009 REMARK 465 GLU A 1010 REMARK 465 HIS A 1011 REMARK 465 HIS A 1012 REMARK 465 HIS A 1013 REMARK 465 HIS A 1014 REMARK 465 HIS A 1015 REMARK 465 HIS A 1016 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 THR A 939 -150.81 -126.62 REMARK 500 REMARK 500 REMARK: NULL DBREF 8FE0 A 808 1010 UNP P22102 PUR2_HUMAN 808 1010 SEQADV 8FE0 MET A 807 UNP P22102 INITIATING METHIONINE SEQADV 8FE0 ALA A 905 UNP P22102 GLN 905 CONFLICT SEQADV 8FE0 HIS A 1011 UNP P22102 EXPRESSION TAG SEQADV 8FE0 HIS A 1012 UNP P22102 EXPRESSION TAG SEQADV 8FE0 HIS A 1013 UNP P22102 EXPRESSION TAG SEQADV 8FE0 HIS A 1014 UNP P22102 EXPRESSION TAG SEQADV 8FE0 HIS A 1015 UNP P22102 EXPRESSION TAG SEQADV 8FE0 HIS A 1016 UNP P22102 EXPRESSION TAG SEQRES 1 A 210 MET ALA ARG VAL ALA VAL LEU ILE SER GLY THR GLY SER SEQRES 2 A 210 ASN LEU GLN ALA LEU ILE ASP SER THR ARG GLU PRO ASN SEQRES 3 A 210 SER SER ALA GLN ILE ASP ILE VAL ILE SER ASN LYS ALA SEQRES 4 A 210 ALA VAL ALA GLY LEU ASP LYS ALA GLU ARG ALA GLY ILE SEQRES 5 A 210 PRO THR ARG VAL ILE ASN HIS LYS LEU TYR LYS ASN ARG SEQRES 6 A 210 VAL GLU PHE ASP SER ALA ILE ASP LEU VAL LEU GLU GLU SEQRES 7 A 210 PHE SER ILE ASP ILE VAL CYS LEU ALA GLY PHE MET ARG SEQRES 8 A 210 ILE LEU SER GLY PRO PHE VAL ALA LYS TRP ASN GLY LYS SEQRES 9 A 210 MET LEU ASN ILE HIS PRO SER LEU LEU PRO SER PHE LYS SEQRES 10 A 210 GLY SER ASN ALA HIS GLU GLN ALA LEU GLU THR GLY VAL SEQRES 11 A 210 THR VAL THR GLY CYS THR VAL HIS PHE VAL ALA GLU ASP SEQRES 12 A 210 VAL ASP ALA GLY GLN ILE ILE LEU GLN GLU ALA VAL PRO SEQRES 13 A 210 VAL LYS ARG GLY ASP THR VAL ALA THR LEU SER GLU ARG SEQRES 14 A 210 VAL LYS LEU ALA GLU HIS LYS ILE PHE PRO ALA ALA LEU SEQRES 15 A 210 GLN LEU VAL ALA SER GLY THR VAL GLN LEU GLY GLU ASN SEQRES 16 A 210 GLY LYS ILE CYS TRP VAL LYS GLU GLU HIS HIS HIS HIS SEQRES 17 A 210 HIS HIS HET GAR A1101 31 HET XSO A1102 34 HETNAM GAR GLYCINAMIDE RIBONUCLEOTIDE HETNAM XSO N-{5-[4-(2-AMINO-4-OXO-1,4-DIHYDROTHIENO[2,3- HETNAM 2 XSO D]PYRIMIDIN-6-YL)BUTYL]-3-FLUOROPYRIDINE-2-CARBONYL}- HETNAM 3 XSO L-GLUTAMIC ACID FORMUL 2 GAR C7 H13 N2 O8 P 2- FORMUL 3 XSO C21 H22 F N5 O6 S FORMUL 4 HOH *106(H2 O) HELIX 1 AA1 GLY A 818 ARG A 829 1 12 HELIX 2 AA2 VAL A 847 ALA A 856 1 10 HELIX 3 AA3 ASN A 864 TYR A 868 5 5 HELIX 4 AA4 ASN A 870 PHE A 885 1 16 HELIX 5 AA5 SER A 900 TRP A 907 1 8 HELIX 6 AA6 ASN A 926 GLY A 935 1 10 HELIX 7 AA7 THR A 968 SER A 993 1 26 SHEET 1 AA1 7 THR A 860 VAL A 862 0 SHEET 2 AA1 7 GLN A 836 SER A 842 1 N SER A 842 O ARG A 861 SHEET 3 AA1 7 ARG A 809 ILE A 814 1 N ILE A 814 O ILE A 841 SHEET 4 AA1 7 ILE A 889 LEU A 892 1 O CYS A 891 N ALA A 811 SHEET 5 AA1 7 MET A 911 HIS A 915 1 O LEU A 912 N LEU A 892 SHEET 6 AA1 7 VAL A 938 PHE A 945 -1 O THR A 942 N HIS A 915 SHEET 7 AA1 7 ILE A 955 PRO A 962 -1 O ILE A 956 N VAL A 943 SHEET 1 AA2 2 VAL A 996 LEU A 998 0 SHEET 2 AA2 2 ILE A1004 TRP A1006 -1 O CYS A1005 N GLN A 997 CISPEP 1 LEU A 919 PRO A 920 0 11.46 CRYST1 74.879 74.879 100.616 90.00 90.00 120.00 P 32 2 1 6 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 0.013355 0.007710 0.000000 0.00000 SCALE2 0.000000 0.015421 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009939 0.00000