HEADER TRANSFERASE 17-JAN-22 7WMY TITLE CRYSTAL STRUCTURE OF METHYLENETETRAHYDROFOLATE REDUCTASE MSMEG_6649 TITLE 2 FROM MYCOBACTERIUM SMEGMATIS WITH 5-METHYLTETRAHYDROFOLATE 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 7WMY 1 REMARK REVDAT 2 09-AUG-23 7WMY 1 JRNL REVDAT 1 25-JAN-23 7WMY 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. 2.27 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) : 2.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 21054 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1052 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 37.1650 - 4.5302 1.00 2650 135 0.1953 0.2313 REMARK 3 2 4.5302 - 3.5967 1.00 2521 155 0.1747 0.1920 REMARK 3 3 3.5967 - 3.1423 1.00 2533 116 0.2138 0.2511 REMARK 3 4 3.1423 - 2.8551 1.00 2494 136 0.2378 0.2716 REMARK 3 5 2.8551 - 2.6505 0.95 2345 136 0.2490 0.2886 REMARK 3 6 2.6505 - 2.4943 1.00 2497 119 0.2539 0.2811 REMARK 3 7 2.4943 - 2.3694 1.00 2487 115 0.2567 0.3063 REMARK 3 8 2.3694 - 2.2663 1.00 2475 140 0.2635 0.2745 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.530 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.23 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 7WMY 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_1300026676. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL02U1 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 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21092 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.266 REMARK 200 RESOLUTION RANGE LOW (A) : 60.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : 0.12200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.30 REMARK 200 R MERGE FOR SHELL (I) : 1.33200 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 (%): 63.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CACODYLATE, CALCIUM ACETATE, REMARK 280 GLYCEROL, PEG 8000, PH 7.2, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 34.86433 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 69.72867 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 69.72867 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 34.86433 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 ARG A 296 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 MET A 50 CG SD CE REMARK 470 GLU A 52 CG CD OE1 OE2 REMARK 470 GLU A 53 CG CD OE1 OE2 REMARK 470 ASP A 54 CG OD1 OD2 REMARK 470 MET A 61 CG SD CE REMARK 470 ARG A 95 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 123 CG OD1 OD2 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 MET A 61 84.60 71.03 REMARK 500 ASP A 123 -149.04 -114.08 REMARK 500 VAL A 260 -39.73 -130.51 REMARK 500 REMARK 500 REMARK: NULL DBREF 7WMY 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 *64(H2 O) HELIX 1 AA1 GLY A 18 ALA A 36 1 19 HELIX 2 AA2 ASP A 66 LEU A 78 1 13 HELIX 3 AA3 GLY A 93 HIS A 107 1 15 HELIX 4 AA4 ALA A 130 PHE A 138 1 9 HELIX 5 AA5 ASP A 155 GLU A 166 1 12 HELIX 6 AA6 ASP A 179 THR A 192 1 14 HELIX 7 AA7 PRO A 206 GLU A 211 5 6 HELIX 8 AA8 GLY A 213 ILE A 219 1 7 HELIX 9 AA9 GLY A 225 SER A 240 1 16 HELIX 10 AB1 GLU A 241 GLY A 259 1 19 HELIX 11 AB2 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 47 SHEET 4 AA1 9 PHE A 109 VAL A 115 1 O GLU A 110 N GLY A 83 SHEET 5 AA1 9 HIS A 144 LEU A 149 1 O GLY A 146 N ILE A 112 SHEET 6 AA1 9 PHE A 170 THR A 173 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 SER A 268 N ILE A 198 SHEET 9 AA1 9 VAL A 6 GLU A 9 1 N ALA A 7 O LEU A 269 CRYST1 85.830 85.830 104.593 90.00 90.00 120.00 P 31 2 1 6 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 0.011651 0.006727 0.000000 0.00000 SCALE2 0.000000 0.013453 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009561 0.00000