HEADER TRANSFERASE 17-JAN-22 7WMW TITLE CRYSTAL STRUCTURE OF METHYLENETETRAHYDROFOLATE REDUCTASE MSMEG_6649 TITLE 2 FROM MYCOBACTERIUM SMEGMATIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYLENETETRAHYDROFOLATE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOLICIBACTERIUM SMEGMATIS MC2 155; SOURCE 3 ORGANISM_TAXID: 246196; SOURCE 4 STRAIN: ATCC 700084 / MC(2)155; SOURCE 5 GENE: MSMEG_6649; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS METHYLENETETRAHYDROFOLATE REDUCTASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR W.LIN,W.WANG REVDAT 3 29-MAY-24 7WMW 1 REMARK REVDAT 2 09-AUG-23 7WMW 1 JRNL REVDAT 1 25-JAN-23 7WMW 0 JRNL AUTH J.LI,M.YANG,W.LI,C.LU,D.FENG,Z.SHANG,C.WANG,W.LIN JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF A JRNL TITL 2 MYCOBACTERIAL METHYLENETETRAHYDROFOLATE REDUCTASE UTILIZING JRNL TITL 3 NADH AS THE EXCLUSIVE COFACTOR. JRNL REF BIOCHEM.J. V. 480 1129 2023 JRNL REFN ESSN 1470-8728 JRNL PMID 37435857 JRNL DOI 10.1042/BCJ20230138 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 36223 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 3625 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 32.6010 - 6.0682 0.99 1252 134 0.1755 0.1800 REMARK 3 2 6.0682 - 4.8215 1.00 1257 140 0.1853 0.2172 REMARK 3 3 4.8215 - 4.2135 1.00 1251 144 0.1631 0.1838 REMARK 3 4 4.2135 - 3.8289 1.00 1268 144 0.1851 0.2127 REMARK 3 5 3.8289 - 3.5548 1.00 1241 137 0.2175 0.2517 REMARK 3 6 3.5548 - 3.3455 1.00 1265 141 0.2398 0.2834 REMARK 3 7 3.3455 - 3.1781 1.00 1256 136 0.2616 0.2698 REMARK 3 8 3.1781 - 3.0398 1.00 1272 143 0.2818 0.3253 REMARK 3 9 3.0398 - 2.9229 1.00 1250 135 0.2977 0.3455 REMARK 3 10 2.9229 - 2.8221 1.00 1236 139 0.3148 0.3174 REMARK 3 11 2.8221 - 2.7339 1.00 1273 137 0.2967 0.3124 REMARK 3 12 2.7339 - 2.6558 1.00 1244 142 0.2988 0.3446 REMARK 3 13 2.6558 - 2.5859 1.00 1259 139 0.2973 0.3642 REMARK 3 14 2.5859 - 2.5228 1.00 1247 138 0.3035 0.3815 REMARK 3 15 2.5228 - 2.4655 1.00 1268 140 0.2914 0.3719 REMARK 3 16 2.4655 - 2.4130 1.00 1229 141 0.2745 0.2798 REMARK 3 17 2.4130 - 2.3648 1.00 1296 145 0.2952 0.3020 REMARK 3 18 2.3648 - 2.3202 1.00 1249 142 0.3331 0.3875 REMARK 3 19 2.3202 - 2.2787 1.00 1242 136 0.3177 0.3738 REMARK 3 20 2.2787 - 2.2401 1.00 1260 141 0.3677 0.3677 REMARK 3 21 2.2401 - 2.2040 1.00 1254 137 0.3458 0.4083 REMARK 3 22 2.2040 - 2.1701 1.00 1262 139 0.3451 0.3672 REMARK 3 23 2.1701 - 2.1382 1.00 1242 138 0.3767 0.3851 REMARK 3 24 2.1382 - 2.1081 1.00 1253 144 0.3880 0.3906 REMARK 3 25 2.1081 - 2.0796 1.00 1255 139 0.4146 0.4241 REMARK 3 26 2.0796 - 2.0530 0.98 1217 134 0.4301 0.4020 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) : 33.260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.50 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7WMW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1300026655. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36223 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 16.00 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.4700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 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: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, BIS-TRIS, PEG 3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 65.20250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.90750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.90750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.60125 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.90750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.90750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 97.80375 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.90750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.90750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 32.60125 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.90750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.90750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 97.80375 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 65.20250 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 ILE A 51 REMARK 465 GLU A 52 REMARK 465 GLU A 53 REMARK 465 ASP A 54 REMARK 465 ASP A 55 REMARK 465 GLY A 56 REMARK 465 ARG A 57 REMARK 465 PRO A 58 REMARK 465 VAL A 59 REMARK 465 GLU A 60 REMARK 465 MET A 61 REMARK 465 LYS A 62 REMARK 465 PRO A 63 REMARK 465 LYS A 64 REMARK 465 PRO A 118 REMARK 465 ARG A 119 REMARK 465 THR A 120 REMARK 465 MET A 121 REMARK 465 THR A 122 REMARK 465 ASP A 123 REMARK 465 GLY A 124 REMARK 465 GLU A 125 REMARK 465 GLY A 126 REMARK 465 ALA A 127 REMARK 465 ARG A 296 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 39 14.95 -67.78 REMARK 500 VAL A 260 -46.37 -135.37 REMARK 500 REMARK 500 REMARK: NULL DBREF 7WMW A 1 296 UNP A0R6S0 A0R6S0_MYCS2 1 296 SEQRES 1 A 296 MET THR LEU ASN THR VAL ALA LEU GLU LEU VAL PRO SER SEQRES 2 A 296 ASN LEU ASP LEU GLY THR ALA HIS ALA LEU ALA GLU LEU SEQRES 3 A 296 GLN LYS VAL ARG LYS LEU ALA VAL ASP ALA GLY LEU ASP SEQRES 4 A 296 GLY ARG ILE ARG HIS ILE MET ILE PRO GLY MET ILE GLU SEQRES 5 A 296 GLU ASP ASP GLY ARG PRO VAL GLU MET LYS PRO LYS LEU SEQRES 6 A 296 ASP VAL LEU ASP TYR TRP GLU LEU VAL GLN ARG GLU LEU SEQRES 7 A 296 PRO ASP VAL ARG GLY LEU CYS THR GLN VAL THR SER PHE SEQRES 8 A 296 LEU GLY GLU ARG SER LEU ARG ARG ARG LEU THR ALA LEU SEQRES 9 A 296 ILE GLN HIS GLY PHE GLU GLY ILE ALA PHE VAL GLY VAL SEQRES 10 A 296 PRO ARG THR MET THR ASP GLY GLU GLY ALA GLY VAL ALA SEQRES 11 A 296 PRO THR ASP ALA LEU SER THR PHE SER HIS LEU VAL LYS SEQRES 12 A 296 HIS ARG GLY VAL ILE LEU ILE PRO THR ARG ASP ASP GLU SEQRES 13 A 296 LEU SER ARG PHE GLY PHE LYS CYS LYS GLU GLY ALA THR SEQRES 14 A 296 PHE GLY MET THR GLN LEU LEU TYR SER ASP ALA ILE VAL SEQRES 15 A 296 ASN PHE LEU THR GLU PHE SER ARG ASN THR ASP HIS ARG SEQRES 16 A 296 PRO GLU ILE LEU LEU SER PHE GLY PHE VAL PRO LYS MET SEQRES 17 A 296 GLU SER GLU VAL GLY LEU ILE ASP TRP LEU ILE GLN ASP SEQRES 18 A 296 PRO ASP ASN GLY ALA VAL ALA THR GLU GLN GLN PHE VAL SEQRES 19 A 296 ARG ARG LEU ALA ALA SER GLU PRO ALA GLN LYS ARG ALA SEQRES 20 A 296 GLN MET LEU ASP LEU TYR LYS ARG VAL ILE ASP GLY VAL SEQRES 21 A 296 ILE ASP LEU GLY PHE PRO VAL SER LEU HIS PHE GLU ALA SEQRES 22 A 296 PRO TYR GLY VAL SER ALA PRO ALA PHE GLU THR PHE ALA SEQRES 23 A 296 ALA MET LEU ASP TYR TRP ALA PRO ASP ARG FORMUL 2 HOH *41(H2 O) HELIX 1 AA1 ASN A 14 LEU A 17 5 4 HELIX 2 AA2 GLY A 18 ALA A 36 1 19 HELIX 3 AA3 ASP A 66 LEU A 78 1 13 HELIX 4 AA4 GLY A 93 HIS A 107 1 15 HELIX 5 AA5 ALA A 130 PHE A 138 1 9 HELIX 6 AA6 ASP A 155 GLU A 166 1 12 HELIX 7 AA7 ASP A 179 THR A 192 1 14 HELIX 8 AA8 MET A 208 GLY A 213 1 6 HELIX 9 AA9 GLY A 213 ILE A 219 1 7 HELIX 10 AB1 GLY A 225 SER A 240 1 16 HELIX 11 AB2 GLU A 241 GLY A 259 1 19 HELIX 12 AB3 SER A 278 TRP A 292 1 15 SHEET 1 AA1 9 VAL A 6 GLU A 9 0 SHEET 2 AA1 9 HIS A 44 ILE A 47 1 O MET A 46 N LEU A 8 SHEET 3 AA1 9 ARG A 82 VAL A 88 1 O LEU A 84 N ILE A 45 SHEET 4 AA1 9 PHE A 109 VAL A 115 1 O GLU A 110 N GLY A 83 SHEET 5 AA1 9 ARG A 145 LEU A 149 1 O GLY A 146 N PHE A 114 SHEET 6 AA1 9 PHE A 170 LEU A 175 1 O MET A 172 N VAL A 147 SHEET 7 AA1 9 GLU A 197 GLY A 203 1 O LEU A 199 N GLY A 171 SHEET 8 AA1 9 VAL A 267 GLU A 272 1 O HIS A 270 N LEU A 200 SHEET 9 AA1 9 VAL A 6 GLU A 9 1 N ALA A 7 O LEU A 269 CRYST1 67.815 67.815 130.405 90.00 90.00 90.00 P 41 21 2 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 0.014746 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014746 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007668 0.00000