HEADER OXIDOREDUCTASE 06-DEC-19 6V6Y TITLE CRYSTAL STRUCTURE OF T. THERMOPHILUS METHYLENETETRAHYDROFOLATE TITLE 2 DEHYDROGENASE (MTHFD) COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL PROTEIN FOLD; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: METHYLENETETRAHYDROFOLATE DEHYDROGENASE (MTHFD); COMPND 5 EC: 1.5.1.5, 3.5.4.9; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS (STRAIN HB8 / ATCC 27634 / SOURCE 3 DSM 579); SOURCE 4 ORGANISM_TAXID: 300852; SOURCE 5 STRAIN: HB8 / ATCC 27634 / DSM 579; SOURCE 6 GENE: FOLD, TTHA1120; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQTEV KEYWDS AMINO-ACID BIOSYNTHESIS, HISTIDINE BIOSYNTHESIS, HYDROLASE, KEYWDS 2 METHIONINE BIOSYNTHESIS, MULTIFUNCTIONAL ENZYME, NADP, ONE-CARBON KEYWDS 3 METABOLISM, OXIDOREDUCTASE, PURINE BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR F.MAIELLO,C.COELHO,G.GALLO,F.SUCHARSKI,L.HARDY,M.WURTELE REVDAT 2 11-OCT-23 6V6Y 1 REMARK REVDAT 1 27-MAY-20 6V6Y 0 JRNL AUTH F.MAIELLO,G.GALLO,C.COELHO,F.SUCHARSKI,L.HARDY,M.WURTELE JRNL TITL CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS JRNL TITL 2 METHYLENETETRAHYDROFOLATE DEHYDROGENASE AND DETERMINANTS OF JRNL TITL 3 THERMOSTABILITY. JRNL REF PLOS ONE V. 15 32959 2020 JRNL REFN ESSN 1932-6203 JRNL PMID 32401802 JRNL DOI 10.1371/JOURNAL.PONE.0232959 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12-2829-000 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.344 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 3 NUMBER OF REFLECTIONS : 25581 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.015 REMARK 3 FREE R VALUE TEST SET COUNT : 1283 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 39.4219 - 4.4744 0.99 3015 159 0.1823 0.1998 REMARK 3 2 4.4744 - 3.5522 1.00 2954 156 0.1838 0.2272 REMARK 3 3 3.5522 - 3.1034 1.00 2922 154 0.2196 0.2340 REMARK 3 4 3.1034 - 2.8197 1.00 2907 153 0.2397 0.2909 REMARK 3 5 2.8197 - 2.6177 1.00 2918 153 0.2443 0.2901 REMARK 3 6 2.6177 - 2.4634 1.00 2898 153 0.2557 0.2770 REMARK 3 7 2.4634 - 2.3400 0.99 2881 152 0.2757 0.2958 REMARK 3 8 2.3400 - 2.2382 0.90 2591 136 0.3144 0.3640 REMARK 3 9 2.2382 - 2.1520 0.42 1212 67 0.3797 0.4399 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.736 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.87 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.13 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 : 0.008 2217 REMARK 3 ANGLE : 0.975 3024 REMARK 3 CHIRALITY : 0.053 356 REMARK 3 PLANARITY : 0.006 387 REMARK 3 DIHEDRAL : 4.580 1353 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 6V6Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1000245201. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-SEP-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS REMARK 200 BEAMLINE : W01B-MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.4587 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : TOROIDAL BENDABLE REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25688 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.152 REMARK 200 RESOLUTION RANGE LOW (A) : 39.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.3 REMARK 200 DATA REDUNDANCY : 8.530 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.8700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 38.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.96 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.850 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.12-2829-000 REMARK 200 STARTING MODEL: 3P2O REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 800 MM POTASSIUM SODIUM TARTRATE, 100 REMARK 280 MM HEPES BUFFER PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 39.74667 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 19.87333 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 19.87333 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 39.74667 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -39.74667 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 VAL A 167 -69.96 -129.12 REMARK 500 HIS A 186 -171.36 -170.18 REMARK 500 ARG A 276 -71.49 -72.60 REMARK 500 REMARK 500 REMARK: NULL DBREF 6V6Y A 1 277 UNP Q5SJ94 FOLD_THET8 1 277 SEQRES 1 A 277 MET ALA ALA GLN VAL LEU SER GLY HIS GLU ALA ALA GLU SEQRES 2 A 277 ALA VAL TYR GLU GLU ILE ARG ALA ARG LEU ARG SER LEU SEQRES 3 A 277 SER PHE THR PRO SER LEU ARG VAL ILE ARG LEU GLY GLU SEQRES 4 A 277 ASP PRO ALA SER VAL ALA TYR VAL ARG LEU LYS ASP LYS SEQRES 5 A 277 ARG ALA ARG ALA LEU GLY TYR ARG SER GLN VAL GLU VAL SEQRES 6 A 277 TYR PRO GLU ASP LEU PRO GLU GLU ALA LEU LEU GLU ARG SEQRES 7 A 277 ILE ALA ALA LEU ASN ALA ASP GLU GLU VAL ASP GLY ILE SEQRES 8 A 277 LEU VAL GLN LEU PRO LEU PRO PRO HIS ILE ARG THR GLN SEQRES 9 A 277 ARG VAL LEU GLU ALA ILE HIS PRO LEU LYS ASP VAL ASP SEQRES 10 A 277 GLY PHE HIS PRO LEU ASN VAL GLY ARG LEU TRP SER GLY SEQRES 11 A 277 GLY LYS GLY LEU PHE PRO CYS THR PRO LEU GLY VAL VAL SEQRES 12 A 277 ARG LEU LEU LYS HIS TYR GLY VAL ASP LEU ARG GLY LYS SEQRES 13 A 277 GLU VAL VAL VAL VAL GLY ARG SER ASN ILE VAL GLY LYS SEQRES 14 A 277 PRO LEU ALA GLY LEU LEU LEU ARG GLU ASP ALA THR VAL SEQRES 15 A 277 THR LEU ALA HIS SER LYS THR GLN ASP LEU PRO GLU VAL SEQRES 16 A 277 THR ARG ARG ALA GLN VAL LEU VAL VAL ALA VAL GLY ARG SEQRES 17 A 277 PRO HIS LEU VAL ARG LYS GLU TRP VAL ARG GLU GLY ALA SEQRES 18 A 277 ILE VAL VAL ASP VAL GLY VAL ASN ARG VAL GLU GLY ARG SEQRES 19 A 277 LEU LEU GLY ASP VAL HIS PRO GLU VAL ALA GLU VAL ALA SEQRES 20 A 277 PHE ALA LEU THR PRO VAL PRO GLY GLY VAL GLY PRO MET SEQRES 21 A 277 THR VAL ALA MET LEU MET GLY ASN THR LEU GLU ALA ALA SEQRES 22 A 277 LEU LEU ARG ARG HET NAP A 301 48 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 HOH *60(H2 O) HELIX 1 AA1 SER A 7 SER A 25 1 19 HELIX 2 AA2 ASP A 40 GLY A 58 1 19 HELIX 3 AA3 PRO A 71 ASP A 85 1 15 HELIX 4 AA4 ARG A 102 ILE A 110 1 9 HELIX 5 AA5 HIS A 111 ASP A 115 5 5 HELIX 6 AA6 HIS A 120 GLY A 130 1 11 HELIX 7 AA7 PRO A 136 TYR A 149 1 14 HELIX 8 AA8 VAL A 167 GLU A 178 1 12 HELIX 9 AA9 ASP A 191 ARG A 197 1 7 HELIX 10 AB1 ARG A 213 VAL A 217 5 5 HELIX 11 AB2 HIS A 240 VAL A 246 5 7 HELIX 12 AB3 GLY A 256 ARG A 277 1 22 SHEET 1 AA1 6 GLN A 4 VAL A 5 0 SHEET 2 AA1 6 ALA A 249 LEU A 250 1 O LEU A 250 N GLN A 4 SHEET 3 AA1 6 ILE A 222 ASP A 225 1 N VAL A 223 O ALA A 249 SHEET 4 AA1 6 VAL A 201 VAL A 204 1 N LEU A 202 O VAL A 224 SHEET 5 AA1 6 GLU A 157 VAL A 161 1 N VAL A 161 O VAL A 203 SHEET 6 AA1 6 THR A 181 ALA A 185 1 O THR A 181 N VAL A 158 SHEET 1 AA2 3 ARG A 60 TYR A 66 0 SHEET 2 AA2 3 SER A 31 LEU A 37 1 N LEU A 32 O ARG A 60 SHEET 3 AA2 3 GLY A 90 VAL A 93 1 O GLY A 90 N ARG A 33 SHEET 1 AA3 2 ASN A 229 VAL A 231 0 SHEET 2 AA3 2 ARG A 234 LEU A 236 -1 O LEU A 236 N ASN A 229 CISPEP 1 LEU A 95 PRO A 96 0 3.26 CISPEP 2 VAL A 253 PRO A 254 0 0.76 CRYST1 121.357 121.357 59.620 90.00 90.00 120.00 P 32 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 0.008240 0.004757 0.000000 0.00000 SCALE2 0.000000 0.009515 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016773 0.00000