HEADER OXIDOREDUCTASE 28-OCT-22 8BGR TITLE FAD-INDEPENDENT METHYLENE-TETRAHYDROFOLATE REDUCTASE FROM TITLE 2 MYCOBACTERIUM HASSIACUM 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 HASSIACUM; SOURCE 3 ORGANISM_TAXID: 46351; SOURCE 4 STRAIN: DSM 44199 / CIP 105218 / JCM 12690 / 3849; SOURCE 5 GENE: C731_4202, MHAS_04356; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS FAD-INDEPENDENT, NADH-DEPENDENT, METHYLENE-TETRAHYDROFOLATE KEYWDS 2 REDUCTASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.GEHL,U.ERMLER,S.SHIMA REVDAT 3 01-MAY-24 8BGR 1 REMARK REVDAT 2 23-AUG-23 8BGR 1 JRNL REVDAT 1 10-MAY-23 8BGR 0 JRNL AUTH M.GEHL,U.DEMMER,U.ERMLER,S.SHIMA JRNL TITL CRYSTAL STRUCTURE OF FAD-INDEPENDENT JRNL TITL 2 METHYLENE-TETRAHYDROFOLATE REDUCTASE FROM MYCOBACTERIUM JRNL TITL 3 HASSIACUM. JRNL REF PROTEINS V. 91 1329 2023 JRNL REFN ESSN 1097-0134 JRNL PMID 37119125 JRNL DOI 10.1002/PROT.26504 REMARK 2 REMARK 2 RESOLUTION. 1.80 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 25373 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.790 REMARK 3 FREE R VALUE TEST SET COUNT : 1216 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 37.3100 - 3.7400 0.98 3044 158 0.1877 0.1642 REMARK 3 2 3.7400 - 2.9700 0.98 2864 124 0.2101 0.2610 REMARK 3 3 2.9700 - 2.6000 0.99 2792 149 0.2500 0.3064 REMARK 3 4 2.6000 - 2.3600 0.98 2751 148 0.2617 0.3099 REMARK 3 5 2.3600 - 2.1900 0.96 2662 141 0.2740 0.2924 REMARK 3 6 2.1900 - 2.0600 0.94 2636 125 0.2726 0.3074 REMARK 3 7 2.0600 - 1.9600 0.92 2564 112 0.2950 0.3511 REMARK 3 8 1.9600 - 1.8700 0.90 2464 133 0.3227 0.2983 REMARK 3 9 1.8700 - 1.8000 0.88 2380 126 0.3473 0.3932 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) : 0.274 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.779 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.93 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.38 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 : 0.003 2333 REMARK 3 ANGLE : 0.597 3172 REMARK 3 CHIRALITY : 0.043 351 REMARK 3 PLANARITY : 0.004 423 REMARK 3 DIHEDRAL : 12.369 883 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 8BGR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1292126239. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUL-22 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 : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26845 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 94.9 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09300 REMARK 200 FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 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) : 1.11000 REMARK 200 FOR SHELL : 2.000 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: ALPHAFOLD MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 6000, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 281K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 128.70500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 22.89500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 22.89500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 193.05750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 22.89500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 22.89500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 64.35250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 22.89500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 22.89500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 193.05750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 22.89500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 22.89500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 64.35250 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 128.70500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 1 REMARK 465 ASP A 126 REMARK 465 GLY A 127 REMARK 465 GLU A 128 REMARK 465 GLY A 129 REMARK 465 HIS A 130 REMARK 465 GLY A 298 REMARK 465 GLN A 299 REMARK 465 GLY A 300 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 121 170.03 -57.73 REMARK 500 VAL A 145 70.57 50.55 REMARK 500 ASP A 224 77.72 -153.98 REMARK 500 REMARK 500 REMARK: NULL DBREF 8BGR A 1 300 UNP K5BDY6 K5BDY6_MYCHD 1 300 SEQRES 1 A 300 MET THR LEU ASN THR ILE ALA LEU GLU LEU VAL PRO PRO SEQRES 2 A 300 ASN SER ASP GLY PRO ASP GLY GLY ARG GLU GLN ALA VAL SEQRES 3 A 300 GLU ASP ALA ARG LYS VAL LEU ARG CYS ALA ALA GLU THR SEQRES 4 A 300 GLY LEU ALA GLY ARG ILE GLY HIS VAL MET ILE PRO GLY SEQRES 5 A 300 MET ILE GLU GLU ASP PRO ASP ARG PRO ILE PRO MET LYS SEQRES 6 A 300 PRO LYS MET ASP VAL LEU ASP PHE TRP THR ILE ILE ARG SEQRES 7 A 300 PRO GLU LEU PRO GLY ILE ARG GLY LEU CYS THR GLN VAL SEQRES 8 A 300 THR ALA PHE LEU ASP GLU PRO ALA LEU ARG ARG ARG LEU SEQRES 9 A 300 GLY ASP LEU SER ALA ALA GLY PHE ASP GLY ILE ALA PHE SEQRES 10 A 300 VAL GLY VAL PRO ARG THR MET ASN ASP GLY GLU GLY HIS SEQRES 11 A 300 GLY VAL ALA PRO THR ASP ALA LEU SER MET PHE ALA ASP SEQRES 12 A 300 LEU VAL PRO ASN ARG GLY ALA ILE LEU ILE PRO THR ARG SEQRES 13 A 300 ASP GLY GLU GLN GLY ARG PHE GLU PHE LYS CYS GLU ARG SEQRES 14 A 300 GLY ALA THR TYR GLY MET THR GLN LEU LEU TYR SER ASP SEQRES 15 A 300 ALA ILE VAL GLY PHE LEU ARG GLU PHE ALA ARG ARG THR SEQRES 16 A 300 ASP HIS ARG PRO GLU ILE LEU LEU SER PHE GLY PHE VAL SEQRES 17 A 300 PRO LYS LEU GLU ALA LYS VAL GLY LEU ILE ASN TRP LEU SEQRES 18 A 300 ILE GLN ASP PRO GLY ASN PRO ALA VAL ALA ALA GLU GLN SEQRES 19 A 300 GLU PHE VAL ARG ARG LEU ALA GLY LEU GLU PRO ALA ASP SEQRES 20 A 300 LYS ARG LYS LEU MET VAL ASP LEU TYR LYS ARG VAL ILE SEQRES 21 A 300 ASP GLY VAL ALA ASP LEU GLY PHE PRO LEU SER VAL HIS SEQRES 22 A 300 LEU GLU ALA THR TYR GLY VAL SER VAL PRO ALA PHE GLU SEQRES 23 A 300 THR PHE ALA GLU MET LEU ALA TYR TRP SER PRO GLY GLN SEQRES 24 A 300 GLY FORMUL 2 HOH *206(H2 O) HELIX 1 AA1 GLY A 21 THR A 39 1 19 HELIX 2 AA2 ASP A 69 ARG A 78 1 10 HELIX 3 AA3 ASP A 96 GLY A 111 1 16 HELIX 4 AA4 ALA A 133 LEU A 138 1 6 HELIX 5 AA5 GLY A 158 ARG A 169 1 12 HELIX 6 AA6 ASP A 182 THR A 195 1 14 HELIX 7 AA7 LEU A 211 GLY A 216 1 6 HELIX 8 AA8 GLY A 216 ILE A 222 1 7 HELIX 9 AA9 ASN A 227 LEU A 243 1 17 HELIX 10 AB1 GLU A 244 ALA A 264 1 21 HELIX 11 AB2 SER A 281 TRP A 295 1 15 SHEET 1 AA1 9 ILE A 6 GLU A 9 0 SHEET 2 AA1 9 HIS A 47 ILE A 50 1 O MET A 49 N LEU A 8 SHEET 3 AA1 9 ARG A 85 VAL A 91 1 O LEU A 87 N VAL A 48 SHEET 4 AA1 9 PHE A 112 VAL A 118 1 O ASP A 113 N GLY A 86 SHEET 5 AA1 9 ASN A 147 LEU A 152 1 O GLY A 149 N ILE A 115 SHEET 6 AA1 9 TYR A 173 THR A 176 1 O MET A 175 N ALA A 150 SHEET 7 AA1 9 GLU A 200 GLY A 206 1 O GLU A 200 N GLY A 174 SHEET 8 AA1 9 LEU A 270 GLU A 275 1 O HIS A 273 N LEU A 203 SHEET 9 AA1 9 ILE A 6 GLU A 9 1 N GLU A 9 O LEU A 274 CRYST1 45.790 45.790 257.410 90.00 90.00 90.00 P 43 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 0.021839 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021839 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003885 0.00000