HEADER OXIDOREDUCTASE/INHIBITOR 21-NOV-22 8F82 TITLE CRYSTAL STRUCTURE OF DIHYDROFOLATE REDUCTASE (DHFR) FROM MYCOBACTERIUM TITLE 2 ULCERANS AGY99 IN COMPLEX WITH NADP AND INHIBITOR MAM845 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROFOLATE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MYULA.01062.A.B13; COMPND 5 EC: 1.5.1.3; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: COMPND 9 MAHHHHHHMTSVGLIWAQSTSGVIGRDGGIPWRLPEDLAHFKRLTMGHTVVMGRRTWDSLPAAHRPLPG COMPND 10 RRNVVVTRQTG LVAHGAQVVGSLEQALSPAEPDAATWVIGGAQIYALALPLANRCEVTEVDVDLPPED COMPND 11 EDALAPVLDQTWAGTSGEWLVSR SGLRYRMHSYRRL 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.B13 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 1 13-DEC-23 8F82 0 JRNL AUTH L.LIU,K.P.BATTAILE,S.LOVELL,B.L.STAKER JRNL TITL CRYSTAL STRUCTURE OF DIHYDROFOLATE REDUCTASE (DHFR) FROM JRNL TITL 2 MYCOBACTERIUM ULCERANS AGY99 IN COMPLEX WITH NADP AND JRNL TITL 3 INHIBITOR MAM845 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.20 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 3 NUMBER OF REFLECTIONS : 47016 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.143 REMARK 3 R VALUE (WORKING SET) : 0.142 REMARK 3 FREE R VALUE : 0.164 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 2290 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 44.0200 - 3.0200 0.99 3127 158 0.1381 0.1550 REMARK 3 2 3.0200 - 2.4000 0.99 3059 168 0.1581 0.1637 REMARK 3 3 2.4000 - 2.1000 0.99 3075 153 0.1500 0.1643 REMARK 3 4 2.1000 - 1.9100 1.00 3047 171 0.1487 0.1774 REMARK 3 5 1.9000 - 1.7700 1.00 3107 132 0.1451 0.1734 REMARK 3 6 1.7700 - 1.6600 1.00 3085 147 0.1416 0.1548 REMARK 3 7 1.6600 - 1.5800 1.00 3038 168 0.1375 0.1612 REMARK 3 8 1.5800 - 1.5100 1.00 3061 137 0.1305 0.1570 REMARK 3 9 1.5100 - 1.4500 1.00 3102 144 0.1333 0.1670 REMARK 3 10 1.4500 - 1.4000 0.99 3051 171 0.1290 0.1542 REMARK 3 11 1.4000 - 1.3600 0.98 2983 139 0.1268 0.1567 REMARK 3 12 1.3600 - 1.3200 0.95 2886 166 0.1272 0.1687 REMARK 3 13 1.3200 - 1.2900 0.88 2717 128 0.1300 0.1698 REMARK 3 14 1.2900 - 1.2500 0.75 2250 143 0.1381 0.1839 REMARK 3 15 1.2500 - 1.2300 0.59 1822 74 0.1427 0.1855 REMARK 3 16 1.2300 - 1.2000 0.43 1316 91 0.1568 0.1857 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.660 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 : 0.006 1701 REMARK 3 ANGLE : 0.962 2365 REMARK 3 CHIRALITY : 0.076 257 REMARK 3 PLANARITY : 0.010 305 REMARK 3 DIHEDRAL : 13.117 687 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 8F82 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_1000270173. 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) : 291 REMARK 200 PH : 6.5 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 : 47045 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 44.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.02800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.23 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.12800 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 (%): 44.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MORPHEUS B4: 12.5%(V/V) MPD, REMARK 280 12.5%(V/V) PEG 1000, 12.5%(W/V) PEG 3350, 100 MM IMIDAZOLE/MES, REMARK 280 PH 6.5, 30 MM NAF, 30 MM NABR AND 30 MM NAI, REMARK 280 MYULA.01062.A.B13.PS38558 AT 10 MG/ML. TRAY: TRAY358B4 MAM777, REMARK 280 PUCK: PUCK HR00407 PIN15, CRYO: DIRECT, VAPOR DIFFUSION, SITTING REMARK 280 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 33.36950 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 THR A 2 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 GLU A 147 CG CD OE1 OE2 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 PRO A 23 39.00 -85.88 REMARK 500 LEU A 26 83.67 -153.02 REMARK 500 REMARK 500 REMARK: NULL DBREF 8F82 A 1 165 UNP A0PQG8 A0PQG8_MYCUA 1 165 SEQADV 8F82 MET A -7 UNP A0PQG8 EXPRESSION TAG SEQADV 8F82 ALA A -6 UNP A0PQG8 EXPRESSION TAG SEQADV 8F82 HIS A -5 UNP A0PQG8 EXPRESSION TAG SEQADV 8F82 HIS A -4 UNP A0PQG8 EXPRESSION TAG SEQADV 8F82 HIS A -3 UNP A0PQG8 EXPRESSION TAG SEQADV 8F82 HIS A -2 UNP A0PQG8 EXPRESSION TAG SEQADV 8F82 HIS A -1 UNP A0PQG8 EXPRESSION TAG SEQADV 8F82 HIS A 0 UNP A0PQG8 EXPRESSION TAG SEQADV 8F82 SER A 89 UNP A0PQG8 CYS 89 ENGINEERED MUTATION SEQADV 8F82 ALA A 96 UNP A0PQG8 GLU 96 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 ALA 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 XJT A 201 34 HET MPD A 202 8 HET NAP A 203 48 HET BR A 204 1 HETNAM XJT 3-{2-[3-({(6M)-2,4-DIAMINO-6-[3-(TRIFLUOROMETHYL) HETNAM 2 XJT PHENYL]PYRIMIDIN-5-YL}OXY)PROPOXY]PHENYL}PROPANOIC HETNAM 3 XJT ACID HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM BR BROMIDE ION HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 XJT C23 H23 F3 N4 O4 FORMUL 3 MPD C6 H14 O2 FORMUL 4 NAP C21 H28 N7 O17 P3 FORMUL 5 BR BR 1- FORMUL 6 HOH *196(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 LEU A 88 1 6 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 ARG A 63 SHEET 4 AA1 8 THR A 97 VAL A 99 1 O TRP A 98 N VAL A 43 SHEET 5 AA1 8 VAL A 4 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 HIS A 160 N VAL A 118 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 ARG A 63 SHEET 4 AA2 8 THR A 97 VAL A 99 1 O TRP A 98 N VAL A 43 SHEET 5 AA2 8 VAL A 4 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 HIS A 160 N VAL A 118 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 -9.43 CISPEP 2 ARG A 57 PRO A 58 0 13.08 CISPEP 3 GLY A 101 GLY A 102 0 2.21 CRYST1 28.666 66.739 44.025 90.00 90.48 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 0.034885 0.000000 0.000292 0.00000 SCALE2 0.000000 0.014984 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022715 0.00000