HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 15-JUL-21 7RGK TITLE DFRA5 COMPLEXED WITH NADPH AND 5-(3-(7-(4-(AMINOMETHYL)PHENYL) TITLE 2 BENZO[D][1,3]DIOXOL-5-YL)BUT-1-YN-1-YL)-6-ETHYLPYRIMIDINE-2,4-DIAMINE TITLE 3 (UCP1223) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROFOLATE REDUCTASE TYPE 5; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DIHYDROFOLATE REDUCTASE TYPE V; COMPND 5 EC: 1.5.1.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: DHFRV; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS INHIBITOR, COMPLEX, ANTIFOLATE, DHFR, OXIDOREDUCTASE, OXIDOREDUCTASE- KEYWDS 2 OXIDOREDUCTASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.N.LOMBARDO,D.L.WRIGHT REVDAT 2 18-OCT-23 7RGK 1 REMARK REVDAT 1 25-MAY-22 7RGK 0 JRNL AUTH J.KRUCINSKA,M.N.LOMBARDO,H.ERLANDSEN,A.ESTRADA,D.SI, JRNL AUTH 2 K.VISWANATHAN,D.L.WRIGHT JRNL TITL STRUCTURE-GUIDED FUNCTIONAL STUDIES OF PLASMID-ENCODED JRNL TITL 2 DIHYDROFOLATE REDUCTASES REVEAL A COMMON MECHANISM OF JRNL TITL 3 TRIMETHOPRIM RESISTANCE IN GRAM-NEGATIVE PATHOGENS. JRNL REF COMMUN BIOL V. 5 459 2022 JRNL REFN ESSN 2399-3642 JRNL PMID 35562546 JRNL DOI 10.1038/S42003-022-03384-Y REMARK 2 REMARK 2 RESOLUTION. 2.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.910 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 22134 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 1066 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 31.4400 - 4.3800 1.00 2725 137 0.1515 0.1971 REMARK 3 2 4.3800 - 3.4800 1.00 2659 132 0.1612 0.1732 REMARK 3 3 3.4800 - 3.0400 1.00 2611 157 0.1901 0.2564 REMARK 3 4 3.0400 - 2.7600 1.00 2589 152 0.2337 0.2767 REMARK 3 5 2.7600 - 2.5600 1.00 2641 104 0.2249 0.3307 REMARK 3 6 2.5600 - 2.4100 1.00 2600 126 0.2514 0.3282 REMARK 3 7 2.4100 - 2.2900 1.00 2649 115 0.2594 0.3018 REMARK 3 8 2.2900 - 2.1900 0.99 2594 143 0.3218 0.3575 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) : 0.311 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.993 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.39 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.07 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 : 0.009 2776 REMARK 3 ANGLE : 1.297 3803 REMARK 3 CHIRALITY : 0.073 399 REMARK 3 PLANARITY : 0.007 460 REMARK 3 DIHEDRAL : 19.419 444 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 7RGK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1000256691. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22144 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.190 REMARK 200 RESOLUTION RANGE LOW (A) : 99.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 1.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 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: 1RX2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MES, LITHIUM SULFATE, PEG 3350, PH 6, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.70300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.55450 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 10.85150 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -68.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 65 -165.45 -104.00 REMARK 500 ASP A 72 3.35 -66.07 REMARK 500 SER B 65 -162.21 -112.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 98 GLY A 99 -129.66 REMARK 500 GLY B 98 GLY B 99 -126.99 REMARK 500 REMARK 500 REMARK: NULL DBREF 7RGK A 1 157 UNP P11731 DYR5_ECOLX 1 157 DBREF 7RGK B 1 157 UNP P11731 DYR5_ECOLX 1 157 SEQRES 1 A 157 MET LYS VAL SER LEU MET ALA ALA LYS ALA LYS ASN GLY SEQRES 2 A 157 VAL ILE GLY CYS GLY PRO HIS ILE PRO TRP SER ALA LYS SEQRES 3 A 157 GLY GLU GLN LEU LEU PHE LYS ALA LEU THR TYR ASN GLN SEQRES 4 A 157 TRP LEU LEU VAL GLY ARG LYS THR PHE GLU SER MET GLY SEQRES 5 A 157 ALA LEU PRO ASN ARG LYS TYR ALA VAL VAL THR ARG SER SEQRES 6 A 157 ALA TRP THR ALA ASP ASN ASP ASN VAL ILE VAL PHE PRO SEQRES 7 A 157 SER ILE GLU GLU ALA MET TYR GLY LEU ALA GLU LEU THR SEQRES 8 A 157 ASP HIS VAL ILE VAL SER GLY GLY GLY GLU ILE TYR ARG SEQRES 9 A 157 GLU THR LEU PRO MET ALA SER THR LEU HIS ILE SER THR SEQRES 10 A 157 ILE ASP ILE GLU PRO GLU GLY ASP VAL PHE PHE PRO ASN SEQRES 11 A 157 ILE PRO ASN THR PHE GLU VAL VAL PHE GLU GLN HIS PHE SEQRES 12 A 157 SER SER ASN ILE ASN TYR CYS TYR GLN ILE TRP GLN LYS SEQRES 13 A 157 GLY SEQRES 1 B 157 MET LYS VAL SER LEU MET ALA ALA LYS ALA LYS ASN GLY SEQRES 2 B 157 VAL ILE GLY CYS GLY PRO HIS ILE PRO TRP SER ALA LYS SEQRES 3 B 157 GLY GLU GLN LEU LEU PHE LYS ALA LEU THR TYR ASN GLN SEQRES 4 B 157 TRP LEU LEU VAL GLY ARG LYS THR PHE GLU SER MET GLY SEQRES 5 B 157 ALA LEU PRO ASN ARG LYS TYR ALA VAL VAL THR ARG SER SEQRES 6 B 157 ALA TRP THR ALA ASP ASN ASP ASN VAL ILE VAL PHE PRO SEQRES 7 B 157 SER ILE GLU GLU ALA MET TYR GLY LEU ALA GLU LEU THR SEQRES 8 B 157 ASP HIS VAL ILE VAL SER GLY GLY GLY GLU ILE TYR ARG SEQRES 9 B 157 GLU THR LEU PRO MET ALA SER THR LEU HIS ILE SER THR SEQRES 10 B 157 ILE ASP ILE GLU PRO GLU GLY ASP VAL PHE PHE PRO ASN SEQRES 11 B 157 ILE PRO ASN THR PHE GLU VAL VAL PHE GLU GLN HIS PHE SEQRES 12 B 157 SER SER ASN ILE ASN TYR CYS TYR GLN ILE TRP GLN LYS SEQRES 13 B 157 GLY HET NAP A 201 48 HET SO4 A 202 5 HET SO4 A 203 5 HET 560 A 204 31 HET NAP B 201 48 HET SO4 B 202 5 HET SO4 B 203 5 HET 560 B 204 62 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM SO4 SULFATE ION HETNAM 560 5-[(3R)-3-{7-[4-(AMINOMETHYL)PHENYL]-2H-1,3- HETNAM 2 560 BENZODIOXOL-5-YL}BUT-1-YN-1-YL]-6-ETHYLPYRIMIDINE-2,4- HETNAM 3 560 DIAMINE HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 3 NAP 2(C21 H28 N7 O17 P3) FORMUL 4 SO4 4(O4 S 2-) FORMUL 6 560 2(C24 H25 N5 O2) FORMUL 11 HOH *41(H2 O) HELIX 1 AA1 GLY A 27 TYR A 37 1 11 HELIX 2 AA2 ARG A 45 GLY A 52 1 8 HELIX 3 AA3 SER A 79 THR A 91 1 13 HELIX 4 AA4 GLY A 99 LEU A 107 1 9 HELIX 5 AA5 PRO A 108 ALA A 110 5 3 HELIX 6 AA6 GLY B 27 TYR B 37 1 11 HELIX 7 AA7 ARG B 45 GLY B 52 1 8 HELIX 8 AA8 SER B 79 THR B 91 1 13 HELIX 9 AA9 GLY B 99 LEU B 107 1 9 HELIX 10 AB1 PRO B 108 ALA B 110 5 3 SHEET 1 AA1 8 VAL A 74 PHE A 77 0 SHEET 2 AA1 8 LYS A 58 VAL A 62 1 N VAL A 61 O PHE A 77 SHEET 3 AA1 8 TRP A 40 GLY A 44 1 N LEU A 41 O LYS A 58 SHEET 4 AA1 8 HIS A 93 GLY A 98 1 O SER A 97 N LEU A 42 SHEET 5 AA1 8 LYS A 2 ALA A 10 1 N SER A 4 O VAL A 96 SHEET 6 AA1 8 THR A 112 ILE A 118 1 O HIS A 114 N LEU A 5 SHEET 7 AA1 8 TYR A 149 LYS A 156 -1 O CYS A 150 N THR A 117 SHEET 8 AA1 8 PHE A 135 PHE A 143 -1 N GLN A 141 O TYR A 151 SHEET 1 AA2 2 VAL A 14 GLY A 16 0 SHEET 2 AA2 2 VAL A 126 PHE A 127 -1 O VAL A 126 N ILE A 15 SHEET 1 AA3 8 VAL B 74 PHE B 77 0 SHEET 2 AA3 8 ARG B 57 VAL B 62 1 N VAL B 61 O PHE B 77 SHEET 3 AA3 8 GLN B 39 GLY B 44 1 N LEU B 41 O ALA B 60 SHEET 4 AA3 8 HIS B 93 GLY B 98 1 O SER B 97 N LEU B 42 SHEET 5 AA3 8 LYS B 2 ALA B 10 1 N SER B 4 O VAL B 96 SHEET 6 AA3 8 THR B 112 ILE B 118 1 O HIS B 114 N ALA B 7 SHEET 7 AA3 8 TYR B 149 LYS B 156 -1 O CYS B 150 N THR B 117 SHEET 8 AA3 8 PHE B 135 PHE B 143 -1 N VAL B 138 O ILE B 153 SHEET 1 AA4 2 VAL B 14 GLY B 16 0 SHEET 2 AA4 2 VAL B 126 PHE B 127 -1 O VAL B 126 N ILE B 15 CRYST1 99.420 99.420 43.406 90.00 90.00 90.00 P 43 8 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 0.010058 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010058 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023038 0.00000