HEADER OXIDOREDUCTASE 12-APR-22 7XI7 TITLE HUMAN DIHYDROFOLATE REDUCTASE COMPLEXED WITH P39 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROFOLATE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.5.1.3; COMPND 5 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: DHFR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS HUMAN DHFR, DIHYDROFOLATE REDUCTASE, P39, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.VANICHTANANKUL,T.SAEYANG,S.KAMCHONWONGPAISAN,J.YUVANIYAMA, AUTHOR 2 Y.YUTHAVONG REVDAT 3 29-NOV-23 7XI7 1 REMARK REVDAT 2 27-JUL-22 7XI7 1 JRNL REVDAT 1 29-JUN-22 7XI7 0 JRNL AUTH J.VANICHTANANKUL,A.YOOMUANG,S.TAWEECHAI,T.SAEYANG,J.PENGON, JRNL AUTH 2 J.YUVANIYAMA,B.TARNCHOMPOO,Y.YUTHAVONG,S.KAMCHONWONGPAISAN JRNL TITL STRUCTURAL INSIGHT INTO EFFECTIVE INHIBITORS' BINDING TO JRNL TITL 2 TOXOPLASMA GONDII DIHYDROFOLATE REDUCTASE THYMIDYLATE JRNL TITL 3 SYNTHASE. JRNL REF ACS CHEM.BIOL. V. 17 1691 2022 JRNL REFN ESSN 1554-8937 JRNL PMID 35715223 JRNL DOI 10.1021/ACSCHEMBIO.1C00627 REMARK 2 REMARK 2 RESOLUTION. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.980 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 47806 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2390 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 22.1800 - 4.2300 0.99 2704 143 0.1560 0.1666 REMARK 3 2 4.2300 - 3.3700 0.99 2719 142 0.1331 0.1288 REMARK 3 3 3.3600 - 2.9400 0.99 2708 144 0.1532 0.2004 REMARK 3 4 2.9400 - 2.6700 0.99 2722 145 0.1742 0.2018 REMARK 3 5 2.6700 - 2.4800 0.99 2636 135 0.1693 0.1856 REMARK 3 6 2.4800 - 2.3300 0.99 2728 143 0.1604 0.2024 REMARK 3 7 2.3300 - 2.2200 0.98 2661 143 0.1606 0.2061 REMARK 3 8 2.2200 - 2.1200 0.98 2675 141 0.1612 0.1926 REMARK 3 9 2.1200 - 2.0400 0.98 2701 141 0.1637 0.2151 REMARK 3 10 2.0400 - 1.9700 0.98 2645 140 0.1579 0.1812 REMARK 3 11 1.9700 - 1.9100 0.98 2634 140 0.1716 0.2009 REMARK 3 12 1.9100 - 1.8500 0.98 2642 143 0.1827 0.2238 REMARK 3 13 1.8500 - 1.8000 0.97 2656 136 0.1945 0.2942 REMARK 3 14 1.8000 - 1.7600 0.97 2641 140 0.2072 0.2657 REMARK 3 15 1.7600 - 1.7200 0.97 2675 137 0.2172 0.2394 REMARK 3 16 1.7200 - 1.6800 0.97 2635 137 0.2248 0.2349 REMARK 3 17 1.6800 - 1.6500 0.97 2634 140 0.2469 0.2964 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.165 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.432 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.40 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 : 0.006 1570 REMARK 3 ANGLE : 0.896 2120 REMARK 3 CHIRALITY : 0.059 222 REMARK 3 PLANARITY : 0.008 271 REMARK 3 DIHEDRAL : 11.962 603 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 7XI7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-APR-22. REMARK 100 THE DEPOSITION ID IS D_1300028209. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLRI REMARK 200 BEAMLINE : BL7.2W REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47806 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 26.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 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: MOLREP REMARK 200 STARTING MODEL: 4DDR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.85 M AMMONIUM SULPHATE, 100 MM REMARK 280 POTASSIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.55000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.98890 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.23667 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 41.55000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 23.98890 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 26.23667 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 41.55000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 23.98890 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 26.23667 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.97781 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 52.47333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 47.97781 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 52.47333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 47.97781 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 52.47333 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: 210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 MET A 0 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 ASP A 110 -84.45 -95.99 REMARK 500 MET A 139 50.04 -92.74 REMARK 500 REMARK 500 REMARK: NULL DBREF 7XI7 A 0 186 UNP P00374 DYR_HUMAN 1 187 SEQRES 1 A 187 MET VAL GLY SER LEU ASN CYS ILE VAL ALA VAL SER GLN SEQRES 2 A 187 ASN MET GLY ILE GLY LYS ASN GLY ASP LEU PRO TRP PRO SEQRES 3 A 187 PRO LEU ARG ASN GLU PHE ARG TYR PHE GLN ARG MET THR SEQRES 4 A 187 THR THR SER SER VAL GLU GLY LYS GLN ASN LEU VAL ILE SEQRES 5 A 187 MET GLY LYS LYS THR TRP PHE SER ILE PRO GLU LYS ASN SEQRES 6 A 187 ARG PRO LEU LYS GLY ARG ILE ASN LEU VAL LEU SER ARG SEQRES 7 A 187 GLU LEU LYS GLU PRO PRO GLN GLY ALA HIS PHE LEU SER SEQRES 8 A 187 ARG SER LEU ASP ASP ALA LEU LYS LEU THR GLU GLN PRO SEQRES 9 A 187 GLU LEU ALA ASN LYS VAL ASP MET VAL TRP ILE VAL GLY SEQRES 10 A 187 GLY SER SER VAL TYR LYS GLU ALA MET ASN HIS PRO GLY SEQRES 11 A 187 HIS LEU LYS LEU PHE VAL THR ARG ILE MET GLN ASP PHE SEQRES 12 A 187 GLU SER ASP THR PHE PHE PRO GLU ILE ASP LEU GLU LYS SEQRES 13 A 187 TYR LYS LEU LEU PRO GLU TYR PRO GLY VAL LEU SER ASP SEQRES 14 A 187 VAL GLN GLU GLU LYS GLY ILE LYS TYR LYS PHE GLU VAL SEQRES 15 A 187 TYR GLU LYS ASN ASP HET 4RI A 201 20 HET SO4 A 202 5 HET SO4 A 203 5 HET SO4 A 204 5 HETNAM 4RI 6-HEXYL-5-PHENYL-PYRIMIDINE-2,4-DIAMINE HETNAM SO4 SULFATE ION FORMUL 2 4RI C16 H22 N4 FORMUL 3 SO4 3(O4 S 2-) FORMUL 6 HOH *293(H2 O) HELIX 1 AA1 LEU A 27 THR A 40 1 14 HELIX 2 AA2 LYS A 54 ILE A 60 1 7 HELIX 3 AA3 PRO A 61 ARG A 65 5 5 HELIX 4 AA4 SER A 92 THR A 100 1 9 HELIX 5 AA5 GLY A 117 ASN A 126 1 10 SHEET 1 AA1 8 PHE A 88 SER A 90 0 SHEET 2 AA1 8 ILE A 71 LEU A 75 1 N VAL A 74 O PHE A 88 SHEET 3 AA1 8 GLN A 47 GLY A 53 1 N VAL A 50 O ILE A 71 SHEET 4 AA1 8 VAL A 109 GLY A 116 1 O TRP A 113 N LEU A 49 SHEET 5 AA1 8 LEU A 4 SER A 11 1 N ASN A 5 O ILE A 114 SHEET 6 AA1 8 HIS A 130 ILE A 138 1 O ILE A 138 N VAL A 10 SHEET 7 AA1 8 ILE A 175 ASN A 185 -1 O LYS A 178 N ARG A 137 SHEET 8 AA1 8 LYS A 157 LEU A 158 -1 N LYS A 157 O GLU A 183 SHEET 1 AA2 8 PHE A 88 SER A 90 0 SHEET 2 AA2 8 ILE A 71 LEU A 75 1 N VAL A 74 O PHE A 88 SHEET 3 AA2 8 GLN A 47 GLY A 53 1 N VAL A 50 O ILE A 71 SHEET 4 AA2 8 VAL A 109 GLY A 116 1 O TRP A 113 N LEU A 49 SHEET 5 AA2 8 LEU A 4 SER A 11 1 N ASN A 5 O ILE A 114 SHEET 6 AA2 8 HIS A 130 ILE A 138 1 O ILE A 138 N VAL A 10 SHEET 7 AA2 8 ILE A 175 ASN A 185 -1 O LYS A 178 N ARG A 137 SHEET 8 AA2 8 GLN A 170 GLU A 172 -1 N GLN A 170 O TYR A 177 SHEET 1 AA3 2 GLY A 15 GLY A 17 0 SHEET 2 AA3 2 THR A 146 PHE A 147 -1 O THR A 146 N ILE A 16 CISPEP 1 ARG A 65 PRO A 66 0 -8.89 CISPEP 2 GLY A 116 GLY A 117 0 0.51 CRYST1 83.100 83.100 78.710 90.00 90.00 120.00 H 3 9 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 0.012034 0.006948 0.000000 0.00000 SCALE2 0.000000 0.013895 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012705 0.00000