HEADER OXIDOREDUCTASE/INHIBITOR 21-NOV-22 8F83 TITLE CRYSTAL STRUCTURE OF DIHYDROFOLATE REDUCTASE (DHFR) FROM MYCOBACTERIUM TITLE 2 ULCERANS AGY99 IN COMPLEX WITH NADP AND INHIBITOR MAM846 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROFOLATE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MYULA.01062.A.B11; COMPND 5 EC: 1.5.1.3; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM ULCERANS; SOURCE 3 ORGANISM_TAXID: 362242; SOURCE 4 STRAIN: AGY99; SOURCE 5 GENE: DFRA, MUL_2179; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: MYULA.01062.A.B11 KEYWDS SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR KEYWDS 2 INFECTIOUS DISEASE, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR COMPLEX, KEYWDS 3 OXIDOREDUCTASE, OXIDOREDUCTASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE,SEATTLE AUTHOR 2 STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE (SSGCID) REVDAT 3 06-NOV-24 8F83 1 JRNL REVDAT 2 19-JUN-24 8F83 1 REMARK REVDAT 1 13-DEC-23 8F83 0 JRNL AUTH M.ANDRADE MEIRELLES,V.M.ALMEIDA,J.R.SULLIVAN,I.DE TOLEDO, JRNL AUTH 2 C.V.DOS REIS,M.R.CUNHA,R.ZIGWEID,A.SHIM,B.SANKARAN, JRNL AUTH 3 E.L.WOODWARD,S.SEIBOLD,L.LIU,M.R.MIAN,K.P.BATTAILE,J.RILEY, JRNL AUTH 4 C.DUNCAN,F.R.C.SIMEONS,L.FERGUSON,H.JOJI,K.D.READ,S.LOVELL, JRNL AUTH 5 B.L.STAKER,M.A.BEHR,R.A.PILLI,R.M.COUNAGO JRNL TITL RATIONAL EXPLORATION OF 2,4-DIAMINOPYRIMIDINES AS DHFR JRNL TITL 2 INHIBITORS ACTIVE AGAINST MYCOBACTERIUM ABSCESSUS AND JRNL TITL 3 MYCOBACTERIUM AVIUM , TWO EMERGING HUMAN PATHOGENS. JRNL REF J.MED.CHEM. 2024 JRNL REFN ISSN 0022-2623 JRNL PMID 39468773 JRNL DOI 10.1021/ACS.JMEDCHEM.4C01594 REMARK 2 REMARK 2 RESOLUTION. 1.32 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 31527 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1583 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 35.3800 - 2.9400 0.99 2797 149 0.1342 0.1323 REMARK 3 2 2.9300 - 2.3300 0.99 2768 139 0.1538 0.1922 REMARK 3 3 2.3300 - 2.0400 0.99 2740 150 0.1504 0.1915 REMARK 3 4 2.0400 - 1.8500 0.99 2741 157 0.1493 0.1902 REMARK 3 5 1.8500 - 1.7200 1.00 2722 146 0.1487 0.1881 REMARK 3 6 1.7200 - 1.6200 0.99 2792 123 0.1601 0.2156 REMARK 3 7 1.6200 - 1.5300 0.99 2732 151 0.1589 0.2504 REMARK 3 8 1.5300 - 1.4700 0.99 2743 152 0.1754 0.2177 REMARK 3 9 1.4700 - 1.4100 0.99 2735 145 0.1823 0.2523 REMARK 3 10 1.4100 - 1.3600 0.95 2663 129 0.2090 0.2889 REMARK 3 11 1.3600 - 1.3200 0.93 2511 142 0.2278 0.2783 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.950 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 : 0.010 1427 REMARK 3 ANGLE : 1.203 1968 REMARK 3 CHIRALITY : 0.080 216 REMARK 3 PLANARITY : 0.019 247 REMARK 3 DIHEDRAL : 10.919 273 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 8F83 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1000270174. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31584 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.320 REMARK 200 RESOLUTION RANGE LOW (A) : 35.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.34 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.55500 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PACT B4: 0.1M MIB (SODIUM MALONATE REMARK 280 DIBASIC MONOHYDRATE, IMIDAZOLE, BORIC ACID) PH 7, REMARK 280 MYULA.01062.A.B11.PS38558 AT 10 MG/ML. TRAY: TRAY358B4 MAM846, REMARK 280 PUCK: PUCK HR00407 PIN15, CRYO: 20% PEG 300, PH 7.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 35.37900 REMARK 290 SMTRY3 2 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 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 -7 REMARK 465 ALA A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 91 REMARK 465 GLU A 92 REMARK 465 PRO A 93 REMARK 465 ASP A 94 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 THR A 2 OG1 CG2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 57 0.13 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8F83 A 1 165 UNP A0PQG8 A0PQG8_MYCUA 1 165 SEQADV 8F83 MET A -7 UNP A0PQG8 INITIATING METHIONINE SEQADV 8F83 ALA A -6 UNP A0PQG8 EXPRESSION TAG SEQADV 8F83 HIS A -5 UNP A0PQG8 EXPRESSION TAG SEQADV 8F83 HIS A -4 UNP A0PQG8 EXPRESSION TAG SEQADV 8F83 HIS A -3 UNP A0PQG8 EXPRESSION TAG SEQADV 8F83 HIS A -2 UNP A0PQG8 EXPRESSION TAG SEQADV 8F83 HIS A -1 UNP A0PQG8 EXPRESSION TAG SEQADV 8F83 HIS A 0 UNP A0PQG8 EXPRESSION TAG SEQADV 8F83 SER A 89 UNP A0PQG8 CYS 89 ENGINEERED MUTATION SEQRES 1 A 173 MET ALA HIS HIS HIS HIS HIS HIS MET THR SER VAL GLY SEQRES 2 A 173 LEU ILE TRP ALA GLN SER THR SER GLY VAL ILE GLY ARG SEQRES 3 A 173 ASP GLY GLY ILE PRO TRP ARG LEU PRO GLU ASP LEU ALA SEQRES 4 A 173 HIS PHE LYS ARG LEU THR MET GLY HIS THR VAL VAL MET SEQRES 5 A 173 GLY ARG ARG THR TRP ASP SER LEU PRO ALA ALA HIS ARG SEQRES 6 A 173 PRO LEU PRO GLY ARG ARG ASN VAL VAL VAL THR ARG GLN SEQRES 7 A 173 THR GLY LEU VAL ALA HIS GLY ALA GLN VAL VAL GLY SER SEQRES 8 A 173 LEU GLU GLN ALA LEU SER PRO ALA GLU PRO ASP ALA GLU SEQRES 9 A 173 THR TRP VAL ILE GLY GLY ALA GLN ILE TYR ALA LEU ALA SEQRES 10 A 173 LEU PRO LEU ALA ASN ARG CYS GLU VAL THR GLU VAL ASP SEQRES 11 A 173 VAL ASP LEU PRO PRO GLU ASP GLU ASP ALA LEU ALA PRO SEQRES 12 A 173 VAL LEU ASP GLN THR TRP ALA GLY THR SER GLY GLU TRP SEQRES 13 A 173 LEU VAL SER ARG SER GLY LEU ARG TYR ARG MET HIS SER SEQRES 14 A 173 TYR ARG ARG LEU HET NAP A 201 48 HET XJZ A 202 34 HET IMD A 203 5 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM XJZ 3-{2-[3-({2,4-DIAMINO-6-[4-(TRIFLUOROMETHYL) HETNAM 2 XJZ PHENYL]PYRIMIDIN-5-YL}OXY)PROPOXY]PHENYL}PROPANOIC HETNAM 3 XJZ ACID HETNAM IMD IMIDAZOLE HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 XJZ C23 H23 F3 N4 O4 FORMUL 4 IMD C3 H5 N2 1+ FORMUL 5 HOH *181(H2 O) HELIX 1 AA1 LEU A 26 MET A 38 1 13 HELIX 2 AA2 ARG A 46 LEU A 52 1 7 HELIX 3 AA3 PRO A 53 ARG A 57 5 5 HELIX 4 AA4 SER A 83 SER A 89 1 7 HELIX 5 AA5 GLY A 102 LEU A 110 1 9 HELIX 6 AA6 PRO A 111 ALA A 113 5 3 SHEET 1 AA1 8 GLN A 79 VAL A 81 0 SHEET 2 AA1 8 ARG A 63 VAL A 67 1 N VAL A 66 O GLN A 79 SHEET 3 AA1 8 THR A 41 GLY A 45 1 N VAL A 42 O VAL A 65 SHEET 4 AA1 8 GLU A 96 VAL A 99 1 O TRP A 98 N VAL A 43 SHEET 5 AA1 8 SER A 3 SER A 11 1 N GLY A 5 O VAL A 99 SHEET 6 AA1 8 ARG A 115 VAL A 121 1 O THR A 119 N GLN A 10 SHEET 7 AA1 8 ARG A 156 ARG A 164 -1 O TYR A 162 N CYS A 116 SHEET 8 AA1 8 TRP A 141 SER A 145 -1 N ALA A 142 O ARG A 163 SHEET 1 AA2 8 GLN A 79 VAL A 81 0 SHEET 2 AA2 8 ARG A 63 VAL A 67 1 N VAL A 66 O GLN A 79 SHEET 3 AA2 8 THR A 41 GLY A 45 1 N VAL A 42 O VAL A 65 SHEET 4 AA2 8 GLU A 96 VAL A 99 1 O TRP A 98 N VAL A 43 SHEET 5 AA2 8 SER A 3 SER A 11 1 N GLY A 5 O VAL A 99 SHEET 6 AA2 8 ARG A 115 VAL A 121 1 O THR A 119 N GLN A 10 SHEET 7 AA2 8 ARG A 156 ARG A 164 -1 O TYR A 162 N CYS A 116 SHEET 8 AA2 8 LEU A 149 VAL A 150 -1 N LEU A 149 O TYR A 157 SHEET 1 AA3 2 VAL A 15 GLY A 17 0 SHEET 2 AA3 2 ALA A 132 LEU A 133 -1 O ALA A 132 N ILE A 16 CISPEP 1 ARG A 57 PRO A 58 0 2.90 CISPEP 2 SER A 89 PRO A 90 0 -3.58 CISPEP 3 GLY A 101 GLY A 102 0 -0.15 CRYST1 29.225 70.758 36.067 90.00 111.28 90.00 P 1 21 1 2 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 0.034217 0.000000 0.013327 0.00000 SCALE2 0.000000 0.014133 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029755 0.00000